diff --git a/be/src/cloud/cloud_tablet.cpp b/be/src/cloud/cloud_tablet.cpp
index 6c6cadcd082cc6..0da1bbc8b6eb44 100644
--- a/be/src/cloud/cloud_tablet.cpp
+++ b/be/src/cloud/cloud_tablet.cpp
@@ -984,7 +984,9 @@ Status CloudTablet::calc_delete_bitmap_for_compaction(
     if ((config::enable_missing_rows_correctness_check ||
          config::enable_mow_compaction_correctness_check_core) &&
         !allow_delete_in_cumu_compaction &&
-        compaction_type == ReaderType::READER_CUMULATIVE_COMPACTION) {
+        (compaction_type == ReaderType::READER_CUMULATIVE_COMPACTION ||
+         !config::enable_prune_delete_sign_when_base_compaction)) {
+        // also check duplicate key for base compaction when config::enable_prune_delete_sign_when_base_compaction==false
         missed_rows = std::make_unique<RowLocationSet>();
         LOG(INFO) << "RowLocation Set inited succ for tablet:" << tablet_id();
     }
@@ -1005,7 +1007,8 @@ Status CloudTablet::calc_delete_bitmap_for_compaction(
     if (missed_rows) {
         missed_rows_size = missed_rows->size();
         if (!allow_delete_in_cumu_compaction) {
-            if (compaction_type == ReaderType::READER_CUMULATIVE_COMPACTION &&
+            if ((compaction_type == ReaderType::READER_CUMULATIVE_COMPACTION ||
+                 !config::enable_prune_delete_sign_when_base_compaction) &&
                 tablet_state() == TABLET_RUNNING) {
                 if (merged_rows >= 0 && merged_rows != missed_rows_size) {
                     std::string err_msg = fmt::format(
diff --git a/be/src/olap/tablet_reader.cpp b/be/src/olap/tablet_reader.cpp
index a0c3a9c5eda95b..a453634ca8381f 100644
--- a/be/src/olap/tablet_reader.cpp
+++ b/be/src/olap/tablet_reader.cpp
@@ -635,7 +635,8 @@ Status TabletReader::_init_delete_condition(const ReaderParams& read_params) {
     // Delete sign could not be applied when delete on cumu compaction is enabled, bucause it is meant for delete with predicates.
     // If delete design is applied on cumu compaction, it will lose effect when doing base compaction.
     // `_delete_sign_available` indicates the condition where we could apply delete signs to data.
-    _delete_sign_available = ((read_params.reader_type == ReaderType::READER_BASE_COMPACTION &&
+    _delete_sign_available = (((read_params.reader_type == ReaderType::READER_BASE_COMPACTION ||
+                                read_params.reader_type == ReaderType::READER_FULL_COMPACTION) &&
                                config::enable_prune_delete_sign_when_base_compaction) ||
                               read_params.reader_type == ReaderType::READER_COLD_DATA_COMPACTION ||
                               read_params.reader_type == ReaderType::READER_CHECKSUM);
diff --git a/regression-test/data/compaction/test_full_compaction.out b/regression-test/data/compaction/test_full_compaction.out
index b25fdad93145cc..118191b6cc8464 100644
--- a/regression-test/data/compaction/test_full_compaction.out
+++ b/regression-test/data/compaction/test_full_compaction.out
@@ -39,5 +39,4 @@
 -- !select_final --
 1	100
 2	200
-3	0
 
diff --git a/regression-test/data/compaction/test_full_compaction_by_table_id.out b/regression-test/data/compaction/test_full_compaction_by_table_id.out
index b25fdad93145cc..118191b6cc8464 100644
--- a/regression-test/data/compaction/test_full_compaction_by_table_id.out
+++ b/regression-test/data/compaction/test_full_compaction_by_table_id.out
@@ -39,5 +39,4 @@
 -- !select_final --
 1	100
 2	200
-3	0