diff --git a/llvm/lib/ProfileData/InstrProf.cpp b/llvm/lib/ProfileData/InstrProf.cpp
--- a/llvm/lib/ProfileData/InstrProf.cpp
+++ b/llvm/lib/ProfileData/InstrProf.cpp
@@ -1142,8 +1142,16 @@
   const StringRef VarName(INSTR_PROF_QUOTE(INSTR_PROF_RAW_VERSION_VAR));
   Type *IntTy64 = Type::getInt64Ty(M.getContext());
   uint64_t ProfileVersion = (INSTR_PROF_RAW_VERSION | VARIANT_MASK_IR_PROF);
-  if (IsCS)
+  if (IsCS) {
     ProfileVersion |= VARIANT_MASK_CSIR_PROF;
+
+    // The IRPGO flag var (__llvm_profile_raw_version) has external linkage,
+    // it may not be kept if it's non-prevailing for both regular and thin LTO
+    // compilation. This symbol may be accessed in PGO Instrumentation phase
+    // through isIRPGOFlagSet. Keep it may involve too much hassel in multiple
+    // places. Simply set a CSIRPGO module flag to be evaluated instead.
+    M.addModuleFlag(llvm::Module::Warning, "CSIRPGO", 1);
+  }
   if (InstrEntryBBEnabled)
     ProfileVersion |= VARIANT_MASK_INSTR_ENTRY;
   auto IRLevelVersionVariable = new GlobalVariable(
diff --git a/llvm/lib/Transforms/Instrumentation/InstrProfiling.cpp b/llvm/lib/Transforms/Instrumentation/InstrProfiling.cpp
--- a/llvm/lib/Transforms/Instrumentation/InstrProfiling.cpp
+++ b/llvm/lib/Transforms/Instrumentation/InstrProfiling.cpp
@@ -757,13 +757,32 @@
   CoverageNamesVar->eraseFromParent();
 }
 
+static uint64_t getIntModuleFlagOrZero(const Module &M, StringRef Flag) {
+  auto *MD = dyn_cast_or_null<ConstantAsMetadata>(M.getModuleFlag(Flag));
+  if (!MD)
+    return 0;
+
+  // If the flag is a ConstantAsMetadata, it should be an integer representable
+  // in 64-bits.
+  return cast<ConstantInt>(MD->getValue())->getZExtValue();
+}
+
+static bool enablesIRPGOFlag(const Module &M) {
+  return isIRPGOFlagSet(&M) || getIntModuleFlagOrZero(M, "CSIRPGO") != 0;
+}
+
+static bool enablesValueProfiling(const Module &M) {
+  return enablesIRPGOFlag(M) ||
+         getIntModuleFlagOrZero(M, "EnableValueProfiling") != 0;
+}
+
 /// Get the name of a profiling variable for a particular function.
 static std::string getVarName(InstrProfIncrementInst *Inc, StringRef Prefix) {
   StringRef NamePrefix = getInstrProfNameVarPrefix();
   StringRef Name = Inc->getName()->getName().substr(NamePrefix.size());
   Function *F = Inc->getParent()->getParent();
   Module *M = F->getParent();
-  if (!DoHashBasedCounterSplit || !isIRPGOFlagSet(M) ||
+  if (!DoHashBasedCounterSplit || !enablesIRPGOFlag(*M) ||
       !canRenameComdatFunc(*F))
     return (Prefix + Name).str();
   uint64_t FuncHash = Inc->getHash()->getZExtValue();
@@ -773,20 +792,6 @@
   return (Prefix + Name + "." + Twine(FuncHash)).str();
 }
 
-static uint64_t getIntModuleFlagOrZero(const Module &M, StringRef Flag) {
-  auto *MD = dyn_cast_or_null<ConstantAsMetadata>(M.getModuleFlag(Flag));
-  if (!MD)
-    return 0;
-
-  // If the flag is a ConstantAsMetadata, it should be an integer representable
-  // in 64-bits.
-  return cast<ConstantInt>(MD->getValue())->getZExtValue();
-}
-
-static bool enablesValueProfiling(const Module &M) {
-  return isIRPGOFlagSet(&M) ||
-         getIntModuleFlagOrZero(M, "EnableValueProfiling") != 0;
-}
 
 // Conservatively returns true if data variables may be referenced by code.
 static bool profDataReferencedByCode(const Module &M) {
diff --git a/llvm/test/Transforms/PGOProfile/lto_cspgo_gen.ll b/llvm/test/Transforms/PGOProfile/lto_cspgo_gen.ll
new file mode 100644
--- /dev/null
+++ b/llvm/test/Transforms/PGOProfile/lto_cspgo_gen.ll
@@ -0,0 +1,31 @@
+; REQUIRES: x86-registered-target
+
+; RUN: opt -passes='thinlto-pre-link<O2>' --cs-profilegen-file=alloc -cspgo-kind=cspgo-instr-gen-pipeline -module-summary %s -o %t.bc
+; RUN: llvm-dis %t.bc -o - | FileCheck %s --check-prefix=IRPGO
+
+; RUN: llvm-lto2 run -lto-cspgo-profile-file=alloc -lto-cspgo-gen -save-temps -o %t %t.bc \
+; RUN:   -r=%t.bc,f,px \
+; RUN:   -r=%t.bc,__llvm_profile_filename,x \
+; RUN:   -r=%t.bc,__llvm_profile_raw_version,x
+; RUN: llvm-dis %t.0.0.preopt.bc -o - | FileCheck %s --check-prefix=IRPGO
+
+; IRPGO: {{.*}} !"CSIRPGO", i32 1}
+
+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"
+
+$f = comdat any
+
+; Function Attrs: nofree norecurse nosync nounwind readnone uwtable willreturn mustprogress
+define i32 @f() local_unnamed_addr #0 {
+entry:
+  ret i32 1
+}
+
+attributes #0 = { "target-cpu"="x86-64" }
+
+!llvm.module.flags = !{!0, !1, !2}
+
+!0 = !{i32 1, !"wchar_size", i32 4}
+!1 = !{i32 7, !"uwtable", i32 1}
+!2 = !{i32 1, !"ThinLTO", i32 0}