diff --git a/llvm/include/llvm/Transforms/Utils/SampleProfileLoaderBaseImpl.h b/llvm/include/llvm/Transforms/Utils/SampleProfileLoaderBaseImpl.h
--- a/llvm/include/llvm/Transforms/Utils/SampleProfileLoaderBaseImpl.h
+++ b/llvm/include/llvm/Transforms/Utils/SampleProfileLoaderBaseImpl.h
@@ -87,12 +87,6 @@
 class PseudoProbeManager {
   DenseMap<uint64_t, PseudoProbeDescriptor> GUIDToProbeDescMap;
 
-  const PseudoProbeDescriptor *getDesc(const Function &F) const {
-    auto I = GUIDToProbeDescMap.find(
-        Function::getGUID(FunctionSamples::getCanonicalFnName(F)));
-    return I == GUIDToProbeDescMap.end() ? nullptr : &I->second;
-  }
-
 public:
   PseudoProbeManager(const Module &M) {
     if (NamedMDNode *FuncInfo =
@@ -108,6 +102,24 @@
     }
   }
 
+  const PseudoProbeDescriptor *getDesc(uint64_t GUID) const {
+    auto I = GUIDToProbeDescMap.find(GUID);
+    return I == GUIDToProbeDescMap.end() ? nullptr : &I->second;
+  }
+
+  const PseudoProbeDescriptor *getDesc(StringRef FProfileName) const {
+    return getDesc(Function::getGUID(FProfileName));
+  }
+
+  const PseudoProbeDescriptor *getDesc(const Function &F) const {
+    return getDesc(Function::getGUID(FunctionSamples::getCanonicalFnName(F)));
+  }
+
+  bool profileIsHashMismatched(const PseudoProbeDescriptor &FuncDesc,
+                               const FunctionSamples &Samples) const {
+    return FuncDesc.getFunctionHash() != Samples.getFunctionHash();
+  }
+
   bool moduleIsProbed(const Module &M) const {
     return M.getNamedMetadata(PseudoProbeDescMetadataName);
   }
diff --git a/llvm/lib/Transforms/IPO/SampleProfile.cpp b/llvm/lib/Transforms/IPO/SampleProfile.cpp
--- a/llvm/lib/Transforms/IPO/SampleProfile.cpp
+++ b/llvm/lib/Transforms/IPO/SampleProfile.cpp
@@ -477,6 +477,7 @@
                      std::map<LineLocation, StringRef> &IRAnchors);
   void findProfileAnchors(const FunctionSamples &FS,
                           std::map<LineLocation, StringSet<>> &ProfileAnchors);
+  void countMismatchedSamples(const FunctionSamples &FS);
   void countProfileMismatches(
       const Function &F, const FunctionSamples &FS,
       const std::map<LineLocation, StringRef> &IRAnchors,
@@ -2166,19 +2167,36 @@
   }
 }
 
+void SampleProfileMatcher::countMismatchedSamples(const FunctionSamples &FS) {
+  const auto *FuncDesc = ProbeManager->getDesc(FS.getName());
+  // Skip the function that is external or renamed.
+  if (!FuncDesc)
+    return;
+
+  if (ProbeManager->profileIsHashMismatched(*FuncDesc, FS)) {
+    MismatchedFuncHashSamples += FS.getTotalSamples();
+    return;
+  }
+  for (const auto &I : FS.getCallsiteSamples())
+    for (const auto &CS : I.second)
+      countMismatchedSamples(CS.second);
+}
+
 void SampleProfileMatcher::countProfileMismatches(
     const Function &F, const FunctionSamples &FS,
     const std::map<LineLocation, StringRef> &IRAnchors,
     const std::map<LineLocation, StringSet<>> &ProfileAnchors) {
   bool IsFuncHashMismatch = false;
   if (FunctionSamples::ProfileIsProbeBased) {
-    uint64_t Count = FS.getTotalSamples();
-    TotalFuncHashSamples += Count;
+    TotalFuncHashSamples += FS.getTotalSamples();
     TotalProfiledFunc++;
-    if (!ProbeManager->profileIsValid(F, FS)) {
-      MismatchedFuncHashSamples += Count;
-      NumMismatchedFuncHash++;
-      IsFuncHashMismatch = true;
+    const auto *FuncDesc = ProbeManager->getDesc(F);
+    if (FuncDesc) {
+      if (ProbeManager->profileIsHashMismatched(*FuncDesc, FS)) {
+        NumMismatchedFuncHash++;
+        IsFuncHashMismatch = true;
+      }
+      countMismatchedSamples(FS);
     }
   }
 
diff --git a/llvm/test/Transforms/SampleProfile/Inputs/pseudo-probe-profile-mismatch-nested.prof b/llvm/test/Transforms/SampleProfile/Inputs/pseudo-probe-profile-mismatch-nested.prof
new file mode 100644
--- /dev/null
+++ b/llvm/test/Transforms/SampleProfile/Inputs/pseudo-probe-profile-mismatch-nested.prof
@@ -0,0 +1,12 @@
+main:300:0
+ 1: 0
+ 12: 10 matched:10
+ 20: 10 bar:10
+ 13: bar:200
+  1: 100
+  !CFGChecksum: 123
+ !CFGChecksum: 844635331715433
+bar:11:11
+ 1: 11
+# Original CFGChecksum is 4294967295
+ !CFGChecksum: 123
diff --git a/llvm/test/Transforms/SampleProfile/pseudo-probe-profile-mismatch.ll b/llvm/test/Transforms/SampleProfile/pseudo-probe-profile-mismatch.ll
--- a/llvm/test/Transforms/SampleProfile/pseudo-probe-profile-mismatch.ll
+++ b/llvm/test/Transforms/SampleProfile/pseudo-probe-profile-mismatch.ll
@@ -6,6 +6,9 @@
 ; RUN: llvm-objdump --section-headers %t.obj | FileCheck %s --check-prefix=CHECK-OBJ
 ; RUN: llc < %t.ll -filetype=asm -o - | FileCheck %s --check-prefix=CHECK-ASM
 
+; RUN: opt < %s -passes=sample-profile -sample-profile-file=%S/Inputs/pseudo-probe-profile-mismatch-nested.prof -report-profile-staleness -persist-profile-staleness -S 2>&1 | FileCheck %s --check-prefix=CHECK-NESTED
+
+
 ; CHECK: (1/3) of functions' profile are invalid and (10/50) of samples are discarded due to function hash mismatch.
 ; CHECK: (2/3) of callsites' profile are invalid and (20/30) of samples are discarded due to callsite location mismatch.
 
@@ -47,6 +50,9 @@
 ; CHECK-ASM: .byte 4
 ; CHECK-ASM: .ascii  "MzA="
 
+; CHECK-NESTED: (1/2) of functions' profile are invalid and (211/311) of samples are discarded due to function hash mismatch.
+
+
 target datalayout = "e-m:e-p270:32:32-p271:32:32-p272:64:64-i64:64-f80:128-n8:16:32:64-S128"
 target triple = "x86_64-unknown-linux-gnu"