diff --git a/docs/source/options/mp4_output_options.rst b/docs/source/options/mp4_output_options.rst
index b8cc84da84..582f4cb5d6 100644
--- a/docs/source/options/mp4_output_options.rst
+++ b/docs/source/options/mp4_output_options.rst
@@ -9,9 +9,9 @@ MP4 output options
 
     Deprecated. Do not use.
 
---num_subsegments_per_sidx <number>
+--generate_sidx_in_media_segments
+--nogenerate_sidx_in_media_segments
 
-    Set the number of subsegments in each SIDX box. If 0, a single SIDX box is
-    used per segment; if -1, no SIDX box is used; Otherwise, the muxer packs N
-    subsegments in the root SIDX of the segment, with
-    segment_duration/N/fragment_duration fragments per subsegment.
+    For MP4 with DASH live profile only: Indicates whether to generate 'sidx'
+    box in media segments. Note that it is reuqired by spec if segment template
+    contains $Time$ specifier.
diff --git a/packager/app/muxer_flags.cc b/packager/app/muxer_flags.cc
index 4c31fbdb00..37acec6b0b 100644
--- a/packager/app/muxer_flags.cc
+++ b/packager/app/muxer_flags.cc
@@ -29,14 +29,11 @@ DEFINE_bool(fragment_sap_aligned,
             true,
             "Force fragments to begin with stream access points. This flag "
             "implies segment_sap_aligned.");
-DEFINE_int32(num_subsegments_per_sidx,
-             1,
-             "For ISO BMFF only. Set the number of subsegments in each "
-             "SIDX box. If 0, a single SIDX box is used per segment; if "
-             "-1, no SIDX box is used; Otherwise, the muxer packs N "
-             "subsegments in the root SIDX of the segment, with "
-             "segment_duration/N/fragment_duration fragments per "
-             "subsegment.");
+DEFINE_bool(generate_sidx_in_media_segments,
+            true,
+            "For ISO BMFF with DASH live profile only. Indicates whether to "
+            "generate 'sidx' box in media segments. Note that it is required "
+            "by spec if segment template contains $Time$ specifier.");
 DEFINE_string(temp_dir,
               "",
               "Specify a directory in which to store temporary (intermediate) "
diff --git a/packager/app/muxer_flags.h b/packager/app/muxer_flags.h
index 608529a351..73df416837 100644
--- a/packager/app/muxer_flags.h
+++ b/packager/app/muxer_flags.h
@@ -16,7 +16,7 @@ DECLARE_double(segment_duration);
 DECLARE_bool(segment_sap_aligned);
 DECLARE_double(fragment_duration);
 DECLARE_bool(fragment_sap_aligned);
-DECLARE_int32(num_subsegments_per_sidx);
+DECLARE_bool(generate_sidx_in_media_segments);
 DECLARE_string(temp_dir);
 DECLARE_bool(mp4_include_pssh_in_stream);
 
diff --git a/packager/app/packager_main.cc b/packager/app/packager_main.cc
index f04c235987..5dba8f1802 100644
--- a/packager/app/packager_main.cc
+++ b/packager/app/packager_main.cc
@@ -377,7 +377,8 @@ base::Optional<PackagingParams> GetPackagingParams() {
   }
 
   Mp4OutputParams& mp4_params = packaging_params.mp4_output_params;
-  mp4_params.num_subsegments_per_sidx = FLAGS_num_subsegments_per_sidx;
+  mp4_params.generate_sidx_in_media_segments =
+      FLAGS_generate_sidx_in_media_segments;
   mp4_params.include_pssh_in_stream = FLAGS_mp4_include_pssh_in_stream;
 
   packaging_params.output_media_info = FLAGS_output_media_info;
diff --git a/packager/app/retired_flags.cc b/packager/app/retired_flags.cc
index 8b6c80d2c3..b2c6be8e0f 100644
--- a/packager/app/retired_flags.cc
+++ b/packager/app/retired_flags.cc
@@ -31,6 +31,10 @@ DEFINE_string(playready_key,
 DEFINE_bool(mp4_use_decoding_timestamp_in_timeline,
             false,
             "This flag is deprecated. Do not use.");
+DEFINE_int32(
+    num_subsegments_per_sidx,
+    0,
+    "This flag is deprecated. Use --generate_sidx_in_media_segments instead.");
 
 // The current gflags library does not provide a way to check whether a flag is
 // set in command line. If a flag has a different value to its default value,
@@ -60,6 +64,12 @@ bool InformRetiredDefaultDoubleFlag(const char* flagname, double value) {
   return true;
 }
 
+bool InformRetiredDefaultInt32Flag(const char* flagname, int32_t value) {
+  if (value != 0)
+    fprintf(stderr, "WARNING: %s is deprecated and ignored.\n", flagname);
+  return true;
+}
+
 DEFINE_validator(profile, &InformRetiredStringFlag);
 DEFINE_validator(single_segment, &InformRetiredDefaultTrueFlag);
 DEFINE_validator(webm_subsample_encryption, &InformRetiredDefaultTrueFlag);
@@ -68,3 +78,4 @@ DEFINE_validator(playready_key_id, &InformRetiredStringFlag);
 DEFINE_validator(playready_key, &InformRetiredStringFlag);
 DEFINE_validator(mp4_use_decoding_timestamp_in_timeline,
                  &InformRetiredDefaultFalseFlag);
+DEFINE_validator(num_subsegments_per_sidx, &InformRetiredDefaultInt32Flag);
diff --git a/packager/app/retired_flags.h b/packager/app/retired_flags.h
index bbe235f670..679fe958c9 100644
--- a/packager/app/retired_flags.h
+++ b/packager/app/retired_flags.h
@@ -13,3 +13,4 @@ DECLARE_double(availability_time_offset);
 DECLARE_string(playready_key_id);
 DECLARE_string(playready_key);
 DECLARE_bool(mp4_use_decoding_timestamp_in_timeline);
+DECLARE_int32(num_subsegments_per_sidx);
diff --git a/packager/media/event/mpd_notify_muxer_listener_unittest.cc b/packager/media/event/mpd_notify_muxer_listener_unittest.cc
index 52540ac036..5323d6a33d 100644
--- a/packager/media/event/mpd_notify_muxer_listener_unittest.cc
+++ b/packager/media/event/mpd_notify_muxer_listener_unittest.cc
@@ -46,7 +46,6 @@ MediaInfo ConvertToMediaInfo(const std::string& media_info_string) {
 }
 
 void SetDefaultLiveMuxerOptions(media::MuxerOptions* muxer_options) {
-  muxer_options->mp4_params.num_subsegments_per_sidx = 0;
   muxer_options->output_file_name = "liveinit.mp4";
   muxer_options->segment_template = "live-$NUMBER$.mp4";
   muxer_options->temp_dir.clear();
diff --git a/packager/media/event/muxer_listener_test_helper.cc b/packager/media/event/muxer_listener_test_helper.cc
index e57136fb1e..2c2703fbd5 100644
--- a/packager/media/event/muxer_listener_test_helper.cc
+++ b/packager/media/event/muxer_listener_test_helper.cc
@@ -87,7 +87,6 @@ OnMediaEndParameters GetDefaultOnMediaEndParams() {
 }
 
 void SetDefaultMuxerOptions(MuxerOptions* muxer_options) {
-  muxer_options->mp4_params.num_subsegments_per_sidx = 0;
   muxer_options->output_file_name = "test_output_file_name.mp4";
   muxer_options->segment_template.clear();
   muxer_options->temp_dir.clear();
diff --git a/packager/media/formats/mp4/multi_segment_segmenter.cc b/packager/media/formats/mp4/multi_segment_segmenter.cc
index cf257012c4..0ae18cb13f 100644
--- a/packager/media/formats/mp4/multi_segment_segmenter.cc
+++ b/packager/media/formats/mp4/multi_segment_segmenter.cc
@@ -68,63 +68,6 @@ Status MultiSegmentSegmenter::DoFinalize() {
 }
 
 Status MultiSegmentSegmenter::DoFinalizeSegment() {
-  DCHECK(sidx());
-  // earliest_presentation_time is the earliest presentation time of any
-  // access unit in the reference stream in the first subsegment.
-  // It will be re-calculated later when subsegments are finalized.
-  sidx()->earliest_presentation_time =
-      sidx()->references[0].earliest_presentation_time;
-
-  if (options().mp4_params.num_subsegments_per_sidx <= 0)
-    return WriteSegment();
-
-  // sidx() contains pre-generated segment references with one reference per
-  // fragment. Calculate |num_fragments_per_subsegment| and combine
-  // pre-generated references into final subsegment references.
-  size_t num_fragments = sidx()->references.size();
-  size_t num_fragments_per_subsegment =
-      (num_fragments - 1) / options().mp4_params.num_subsegments_per_sidx + 1;
-  if (num_fragments_per_subsegment <= 1)
-    return WriteSegment();
-
-  size_t frag_index = 0;
-  size_t subseg_index = 0;
-  std::vector<SegmentReference>& refs = sidx()->references;
-  uint64_t first_sap_time =
-      refs[0].sap_delta_time + refs[0].earliest_presentation_time;
-  for (size_t i = 1; i < num_fragments; ++i) {
-    refs[subseg_index].referenced_size += refs[i].referenced_size;
-    refs[subseg_index].subsegment_duration += refs[i].subsegment_duration;
-    refs[subseg_index].earliest_presentation_time =
-        std::min(refs[subseg_index].earliest_presentation_time,
-                 refs[i].earliest_presentation_time);
-    if (refs[subseg_index].sap_type == SegmentReference::TypeUnknown &&
-        refs[i].sap_type != SegmentReference::TypeUnknown) {
-      refs[subseg_index].sap_type = refs[i].sap_type;
-      first_sap_time =
-          refs[i].sap_delta_time + refs[i].earliest_presentation_time;
-    }
-    if (++frag_index >= num_fragments_per_subsegment) {
-      // Calculate sap delta time w.r.t. sidx_->earliest_presentation_time.
-      if (refs[subseg_index].sap_type != SegmentReference::TypeUnknown) {
-        refs[subseg_index].sap_delta_time =
-            first_sap_time - refs[subseg_index].earliest_presentation_time;
-      }
-      if (++i >= num_fragments)
-        break;
-      refs[++subseg_index] = refs[i];
-      first_sap_time =
-          refs[i].sap_delta_time + refs[i].earliest_presentation_time;
-      frag_index = 1;
-    }
-  }
-
-  refs.resize(options().mp4_params.num_subsegments_per_sidx);
-
-  // earliest_presentation_time is the earliest presentation time of any
-  // access unit in the reference stream in the first subsegment.
-  sidx()->earliest_presentation_time = refs[0].earliest_presentation_time;
-
   return WriteSegment();
 }
 
@@ -172,9 +115,15 @@ Status MultiSegmentSegmenter::WriteSegment() {
     styp_->Write(buffer.get());
   }
 
-  // If num_subsegments_per_sidx is negative, no SIDX box is generated.
-  if (options().mp4_params.num_subsegments_per_sidx >= 0)
+  if (options().mp4_params.generate_sidx_in_media_segments) {
+    DCHECK(sidx());
+    DCHECK(!sidx()->references.empty());
+    // earliest_presentation_time is the earliest presentation time of any
+    // access unit in the reference stream in the first subsegment.
+    sidx()->earliest_presentation_time =
+        sidx()->references[0].earliest_presentation_time;
     sidx()->Write(buffer.get());
+  }
 
   const size_t segment_header_size = buffer->Size();
   const size_t segment_size = segment_header_size + fragment_buffer()->Size();
diff --git a/packager/media/formats/mp4/multi_segment_segmenter.h b/packager/media/formats/mp4/multi_segment_segmenter.h
index 5fff12d6c3..b1c524da21 100644
--- a/packager/media/formats/mp4/multi_segment_segmenter.h
+++ b/packager/media/formats/mp4/multi_segment_segmenter.h
@@ -15,19 +15,11 @@ namespace mp4 {
 
 struct SegmentType;
 
-/// Segmenter for MP4 live, main and simple profiles. The generated media file
-/// can contain one or many segments with segment duration defined by @b
-/// MuxerOptions.segment_duration. A segment can contain one or many
-/// subsegments defined by @b num_subsegments_per_sidx. A subsegment can
-/// contain one or many fragments with fragment duration defined by @b
-/// MuxerOptions.fragment_duration. The actual segment or fragment duration
-/// may not match the requested duration exactly, but will be approximated.
-/// That is, the Segmenter tries to end segment/fragment at the first sample
-/// with overall segment/fragment duration not smaller than defined duration
-/// and yet meet SAP requirements. The generated segments are written to files
-/// defined by @b MuxerOptions.segment_template if specified; otherwise,
-/// the segments are appended to the main output file specified by @b
-/// MuxerOptions.output_file_name.
+/// Segmenter for MP4 live, main and simple profiles. There can be multiple
+/// media segments, which can contain multiple fragments. The generated segments
+/// are written to files defined by @b MuxerOptions.segment_template if
+/// specified; otherwise, the segments are appended to the main output file
+/// specified by @b MuxerOptions.output_file_name.
 class MultiSegmentSegmenter : public Segmenter {
  public:
   MultiSegmentSegmenter(const MuxerOptions& options,
diff --git a/packager/media/formats/mp4/single_segment_segmenter.h b/packager/media/formats/mp4/single_segment_segmenter.h
index 37268c2e8f..4659f35435 100644
--- a/packager/media/formats/mp4/single_segment_segmenter.h
+++ b/packager/media/formats/mp4/single_segment_segmenter.h
@@ -25,7 +25,7 @@ namespace mp4 {
 /// is, the Segmenter tries to end subsegment/fragment at the first sample with
 /// overall subsegment/fragment duration not smaller than defined duration and
 /// yet meet SAP requirements. SingleSegmentSegmenter ignores @b
-/// MuxerOptions.num_subsegments_per_sidx.
+/// MuxerOptions.mp4_params.generate_sidx_in_media_segments.
 class SingleSegmentSegmenter : public Segmenter {
  public:
   SingleSegmentSegmenter(const MuxerOptions& options,
diff --git a/packager/media/public/mp4_output_params.h b/packager/media/public/mp4_output_params.h
index dd963cea18..0d286b0d6c 100644
--- a/packager/media/public/mp4_output_params.h
+++ b/packager/media/public/mp4_output_params.h
@@ -11,19 +11,15 @@ namespace shaka {
 
 /// MP4 (ISO-BMFF) output related parameters.
 struct Mp4OutputParams {
-  // Include pssh in the encrypted stream. CMAF and DASH-IF recommends carrying
-  // license acquisition information in the manifest and not duplicate the
-  // information in the stream. (This is not a hard requirement so we are still
-  // CMAF compatible even if pssh is included in the stream.)
+  /// Include pssh in the encrypted stream. CMAF and DASH-IF recommends carrying
+  /// license acquisition information in the manifest and not duplicate the
+  /// information in the stream. (This is not a hard requirement so we are still
+  /// CMAF compatible even if pssh is included in the stream.)
   bool include_pssh_in_stream = true;
-  /// Set the number of subsegments in each SIDX box. If 0, a single SIDX box
-  /// is used per segment. If -1, no SIDX box is used. Otherwise, the Muxer
-  /// will pack N subsegments in the root SIDX of the segment, with
-  /// segment_duration/N/subsegment_duration fragments per subsegment.
-  /// This flag is ingored for DASH MPD with on-demand profile.
-  static constexpr int kNoSidxBoxInSegment = -1;
-  static constexpr int kSingleSidxPerSegment = 0;
-  int num_subsegments_per_sidx = kSingleSidxPerSegment;
+  /// Indicates whether a 'sidx' box should be generated in the media segments.
+  /// Note that it is required by spec if segment_template contains $Times$
+  /// specifier.
+  bool generate_sidx_in_media_segments = true;
 };
 
 }  // namespace shaka