diff --git a/llvm/include/llvm/ProfileData/SampleProf.h b/llvm/include/llvm/ProfileData/SampleProf.h
--- a/llvm/include/llvm/ProfileData/SampleProf.h
+++ b/llvm/include/llvm/ProfileData/SampleProf.h
@@ -1128,7 +1128,8 @@
   void trimAndMergeColdContextProfiles(uint64_t ColdCountThreshold,
                                        bool TrimColdContext,
                                        bool MergeColdContext,
-                                       uint32_t ColdContextFrameLength);
+                                       uint32_t ColdContextFrameLength,
+                                       bool TrimBaseProfileOnly);
   // Canonicalize context profile name and attributes.
   void canonicalizeContextProfiles();
 
diff --git a/llvm/lib/ProfileData/SampleProf.cpp b/llvm/lib/ProfileData/SampleProf.cpp
--- a/llvm/lib/ProfileData/SampleProf.cpp
+++ b/llvm/lib/ProfileData/SampleProf.cpp
@@ -331,7 +331,7 @@
 
 void SampleContextTrimmer::trimAndMergeColdContextProfiles(
     uint64_t ColdCountThreshold, bool TrimColdContext, bool MergeColdContext,
-    uint32_t ColdContextFrameLength) {
+    uint32_t ColdContextFrameLength, bool TrimBaseProfileOnly) {
   if (!TrimColdContext && !MergeColdContext)
     return;
 
@@ -343,10 +343,11 @@
   // container
   std::vector<std::pair<SampleContext, const FunctionSamples *>> ColdProfiles;
   for (const auto &I : ProfileMap) {
+    const SampleContext &Context = I.first;
     const FunctionSamples &FunctionProfile = I.second;
-    if (FunctionProfile.getTotalSamples() >= ColdCountThreshold)
-      continue;
-    ColdProfiles.emplace_back(I.first, &I.second);
+    if (FunctionProfile.getTotalSamples() < ColdCountThreshold &&
+        (!TrimBaseProfileOnly || Context.isBaseContext()))
+      ColdProfiles.emplace_back(Context, &I.second);
   }
 
   // Remove the cold profile from ProfileMap and merge them into
diff --git a/llvm/test/tools/llvm-profgen/cs-preinline.test b/llvm/test/tools/llvm-profgen/cs-preinline.test
--- a/llvm/test/tools/llvm-profgen/cs-preinline.test
+++ b/llvm/test/tools/llvm-profgen/cs-preinline.test
@@ -10,6 +10,11 @@
 ; RUN: llvm-profgen --format=text --perfscript=%S/Inputs/inline-cs-noprobe.perfscript --binary=%S/Inputs/inline-cs-noprobe.perfbin --output=%t --csspgo-preinliner=1  -sample-profile-cold-inline-threshold=0
 ; RUN: FileCheck %s --input-file %t --check-prefix=CHECK-NO-PREINL
 
+; Test cold profile trimming. Only base profiles should be dropped.
+; RUN: llvm-profgen --format=text --perfscript=%S/Inputs/inline-cs-noprobe.perfscript --binary=%S/Inputs/inline-cs-noprobe.perfbin --output=%t --csspgo-preinliner=1  --csprof-trim-cold-context=1 --profile-summary-hot-count=250
+
+; RUN: FileCheck %s --input-file %t --check-prefix=CHECK-TRIM
+
 ; CHECK-DEFAULT:     [main:1 @ foo]:225:0
 ; CHECK-DEFAULT-NEXT: 2.1: 14
 ; CHECK-DEFAULT-NEXT: 3: 15
@@ -39,3 +44,8 @@
 ; CHECK-NO-PREINL-NEXT:[bar]:84:0
 ; CHECK-NO-PREINL-NEXT: 1: 14
 ; CHECK-NO-PREINL-NEXT: !Attributes: 1
+
+; CHECK-TRIM-NOT: [foo]:225:0
+; CHECK-TRIM:[foo:3.1 @ bar]:84:0
+; CHECK-TRIM-NEXT: 1: 14
+; CHECK-TRIM-NEXT: !Attributes: 3
diff --git a/llvm/tools/llvm-profdata/llvm-profdata.cpp b/llvm/tools/llvm-profdata/llvm-profdata.cpp
--- a/llvm/tools/llvm-profdata/llvm-profdata.cpp
+++ b/llvm/tools/llvm-profdata/llvm-profdata.cpp
@@ -759,7 +759,7 @@
     SampleContextTrimmer(ProfileMap)
         .trimAndMergeColdContextProfiles(
             SampleProfColdThreshold, SampleTrimColdContext,
-            SampleMergeColdContext, SampleColdContextFrameDepth);
+            SampleMergeColdContext, SampleColdContextFrameDepth, false);
   }
 
   auto WriterOrErr =
diff --git a/llvm/tools/llvm-profgen/CSPreInliner.cpp b/llvm/tools/llvm-profgen/CSPreInliner.cpp
--- a/llvm/tools/llvm-profgen/CSPreInliner.cpp
+++ b/llvm/tools/llvm-profgen/CSPreInliner.cpp
@@ -252,7 +252,7 @@
   // trim out such profiles from the output.
   std::vector<SampleContext> ProfilesToBeRemoved;
   for (auto &It : ProfileMap) {
-    SampleContext Context = It.second.getContext();
+    SampleContext &Context = It.second.getContext();
     if (!Context.isBaseContext() && !Context.hasState(InlinedContext)) {
       assert(Context.hasState(MergedContext) &&
              "Not inlined context profile should be merged already");
diff --git a/llvm/tools/llvm-profgen/ProfileGenerator.cpp b/llvm/tools/llvm-profgen/ProfileGenerator.cpp
--- a/llvm/tools/llvm-profgen/ProfileGenerator.cpp
+++ b/llvm/tools/llvm-profgen/ProfileGenerator.cpp
@@ -658,16 +658,17 @@
   if (EnableCSPreInliner) {
     CSPreInliner(ProfileMap, *Binary, HotCountThreshold, ColdCountThreshold)
         .run();
+    // Turn off the profile merger by default unless it is explicitly enabled.
+    if (!CSProfMergeColdContext.getNumOccurrences())
+      CSProfMergeColdContext = false;
   }
 
-  // Trim and merge cold context profile using cold threshold above. By default,
-  // we skip such merging and trimming when preinliner is on.
-  if (!EnableCSPreInliner || CSProfTrimColdContext.getNumOccurrences() ||
-      CSProfMergeColdContext.getNumOccurrences()) {
+  // Trim and merge cold context profile using cold threshold above. 
+  if (CSProfTrimColdContext || CSProfMergeColdContext) {
     SampleContextTrimmer(ProfileMap)
         .trimAndMergeColdContextProfiles(
             HotCountThreshold, CSProfTrimColdContext, CSProfMergeColdContext,
-            CSProfMaxColdContextDepth);
+            CSProfMaxColdContextDepth, EnableCSPreInliner);
   }
 }