diff --git a/trunk/auto/setup_variables.sh b/trunk/auto/setup_variables.sh
index 7414e6d07..c7c7c8d4e 100755
--- a/trunk/auto/setup_variables.sh
+++ b/trunk/auto/setup_variables.sh
@@ -10,11 +10,6 @@ if [[ ${SRS_BUILD_TAG} != "" ]]; then
 fi
 echo "SRS_WORKDIR: ${SRS_WORKDIR}, SRS_OBJS_DIR: ${SRS_OBJS_DIR}, SRS_OBJS: ${SRS_OBJS}, SRS_PLATFORM: ${SRS_PLATFORM}"
 
-if [[ $SRS_CLEAN == YES && -f Makefile ]]; then
-    echo "Do full cleanup, you can disable it by: --without-clean"
-    make clean
-fi
-
 # For src object files on each platform.
 (
     mkdir -p ${SRS_OBJS_DIR} && cd ${SRS_OBJS_DIR} &&
diff --git a/trunk/configure b/trunk/configure
index 28ab18db6..855ade2fe 100755
--- a/trunk/configure
+++ b/trunk/configure
@@ -827,6 +827,14 @@ if [ $SRS_EXPORT_LIBRTMP_PROJECT = NO ]; then
     done
 fi
 
+#####################################################################################
+# Do cleanup when configure done.
+#####################################################################################
+if [[ $SRS_CLEAN == YES && -f Makefile ]]; then
+    echo "Do full cleanup, you can disable it by: --without-clean"
+    make clean
+fi
+
 #####################################################################################
 # next step
 #####################################################################################