diff --git a/.github/bot-pr-format-base.sh b/.github/bot-pr-format-base.sh
index d89d3f2ee2a..8d213dcfe69 100644
--- a/.github/bot-pr-format-base.sh
+++ b/.github/bot-pr-format-base.sh
@@ -7,7 +7,26 @@ FORMAT_HEADER_REGEX='^(benchmark|core|cuda|hip|include/ginkgo/core|omp|reference
 FORMAT_REGEX='^(common|examples|test_install)/'
 
 echo "Retrieving PR file list"
-PR_FILES="$(api_get "$PR_URL/files?&per_page=1000" | jq -er '.[] | .filename')"
+PR_FILES=""
+PAGE="1"
+while true; do
+  # this api allows 100 items per page
+  # github action uses `bash -e`. The last empty page will leads jq error, use `|| :` to ignore the error.
+  PR_PAGE_FILES=$(api_get "$PR_URL/files?&per_page=100&page=${PAGE}" | jq -er '.[] | .filename' || :)
+  if [ "${PR_PAGE_FILES}" = "" ]; then
+    break
+  fi
+  echo "Retrieving PR file list - ${PAGE} pages"
+  if [ ! "${PR_FILES}" = "" ]; then
+    # add the same new line format as jq output
+    PR_FILES="${PR_FILES}"$'\n'
+  fi
+  PR_FILES="${PR_FILES}${PR_PAGE_FILES}"
+  PAGE=$(( PAGE + 1 ))
+done
+NUM=$(echo "${PR_FILES}" | wc -l)
+echo "PR has ${NUM} changed files"
+
 TO_FORMAT="$(echo "$PR_FILES" | grep -E $EXTENSION_REGEX || true)"
 
 git remote add fork "$HEAD_URL"
diff --git a/.github/label.sh b/.github/label.sh
index 3cd5023829b..860e520720c 100755
--- a/.github/label.sh
+++ b/.github/label.sh
@@ -3,7 +3,25 @@
 source .github/bot-pr-base.sh
 
 echo "Retrieving PR file list"
-PR_FILES=$(api_get "$PR_URL/files?&per_page=1000" | jq -er '.[] | .filename')
+PR_FILES=""
+PAGE="1"
+while true; do
+  # this api allows 100 items per page
+  # github action uses `bash -e`. The last empty page will leads jq error, use `|| :` to ignore the error.
+  PR_PAGE_FILES=$(api_get "$PR_URL/files?&per_page=100&page=${PAGE}" | jq -er '.[] | .filename' || :)
+  if [ "${PR_PAGE_FILES}" = "" ]; then
+    break
+  fi
+  echo "Retrieving PR file list - ${PAGE} pages"
+  if [ ! "${PR_FILES}" = "" ]; then
+    # add the same new line format as jq output
+    PR_FILES="${PR_FILES}"$'\n'
+  fi
+  PR_FILES="${PR_FILES}${PR_PAGE_FILES}"
+  PAGE=$(( PAGE + 1 ))
+done
+NUM=$(echo "${PR_FILES}" | wc -l)
+echo "PR has ${NUM} changed files"
 
 echo "Retrieving PR label list"
 OLD_LABELS=$(api_get "$ISSUE_URL" | jq -er '[.labels | .[] | .name]')
@@ -17,18 +35,18 @@ label_match() {
 
 LABELS="[]"
 LABELS=$LABELS$(label_match mod:core '(^core/|^include/)')
-LABELS=$LABELS$(label_match mod:reference ^reference/)
-LABELS=$LABELS$(label_match mod:openmp ^omp/)
+LABELS=$LABELS$(label_match mod:reference '^reference/')
+LABELS=$LABELS$(label_match mod:openmp '^omp/')
 LABELS=$LABELS$(label_match mod:cuda '(^cuda/|^common/)')
 LABELS=$LABELS$(label_match mod:hip '(^hip/|^common/)')
-LABELS=$LABELS$(label_match mod:dpcpp ^dpcpp/)
-LABELS=$LABELS$(label_match reg:benchmarking ^benchmark/)
-LABELS=$LABELS$(label_match reg:example ^examples/)
+LABELS=$LABELS$(label_match mod:dpcpp '^dpcpp/')
+LABELS=$LABELS$(label_match reg:benchmarking '^benchmark/')
+LABELS=$LABELS$(label_match reg:example '^examples/')
 LABELS=$LABELS$(label_match reg:build '(cm|CM)ake')
-LABELS=$LABELS$(label_match reg:ci-cd '.yml$')
-LABELS=$LABELS$(label_match reg:documentation ^doc/)
+LABELS=$LABELS$(label_match reg:ci-cd '(^\.github/|\.yml$)')
+LABELS=$LABELS$(label_match reg:documentation '^doc/')
 LABELS=$LABELS$(label_match reg:testing /test/)
-LABELS=$LABELS$(label_match reg:helper-scripts ^dev_tools/)
+LABELS=$LABELS$(label_match reg:helper-scripts '^dev_tools/')
 LABELS=$LABELS$(label_match type:factorization /factorization/)
 LABELS=$LABELS$(label_match type:matrix-format /matrix/)
 LABELS=$LABELS$(label_match type:multigrid /multigrid/)