Index: lib/Transforms/IPO/PassManagerBuilder.cpp
===================================================================
--- lib/Transforms/IPO/PassManagerBuilder.cpp
+++ lib/Transforms/IPO/PassManagerBuilder.cpp
@@ -435,6 +435,12 @@
     MPM.add(createPGOIndirectCallPromotionLegacyPass(/*InLTO = */ true,
                                                      !PGOSampleUse.empty()));
 
+  // For SamplePGO in ThinLTO compile phase, we do not want to unroll loops
+  // as it will change the CFG too much to make the 2nd profile annotation
+  // in backend more difficult.
+  if (PrepareForThinLTO && !PGOSampleUse.empty())
+    DisableUnrollLoops = true;
+
   if (!DisableUnitAtATime) {
     // Infer attributes about declarations if possible.
     MPM.add(createInferFunctionAttrsLegacyPass());
@@ -453,7 +459,10 @@
     MPM.add(createCFGSimplificationPass()); // Clean up after IPCP & DAE
   }
 
-  if (!PerformThinLTO) {
+  // For SamplePGO in ThinLTO compile phase, we do not want to do indirect
+  // call promotion as it will change the CFG too much to make the 2nd
+  // profile annotation in backend more difficult.
+  if (!PerformThinLTO && !(PrepareForThinLTO && !PGOSampleUse.empty())) {
     /// PGO instrumentation is added during the compile phase for ThinLTO, do
     /// not run it a second time
     addPGOInstrPasses(MPM);