diff --git a/llvm/tools/lto/lto.cpp b/llvm/tools/lto/lto.cpp
--- a/llvm/tools/lto/lto.cpp
+++ b/llvm/tools/lto/lto.cpp
@@ -407,6 +407,8 @@
 static void maybeParseOptions(lto_code_gen_t cg) {
   if (!parsedOptions) {
     unwrap(cg)->parseCodeGenDebugOptions();
+    // update the TargetOptions after parsing the debug options.
+    unwrap(cg)->setTargetOptions(InitTargetOptionsFromCodeGenFlags());
     lto_add_attrs(cg);
     parsedOptions = true;
   }