diff --git a/cmds-check.c b/cmds-check.c
index 62aee830..ed8c6984 100644
--- a/cmds-check.c
+++ b/cmds-check.c
@@ -8622,8 +8622,142 @@ static int populate_csum(struct btrfs_trans_handle *trans,
 	return ret;
 }
 
-static int fill_csum_tree(struct btrfs_trans_handle *trans,
-			  struct btrfs_root *csum_root)
+static int fill_csum_tree_from_one_fs_root(struct btrfs_trans_handle *trans,
+				      struct btrfs_root *csum_root,
+				      struct btrfs_root *cur_root)
+{
+	struct btrfs_path *path;
+	struct btrfs_key key;
+	struct extent_buffer *node;
+	struct btrfs_file_extent_item *fi;
+	char *buf = NULL;
+	u64 start = 0;
+	u64 len = 0;
+	int slot = 0;
+	int ret = 0;
+
+	path = btrfs_alloc_path();
+	if (!path)
+		return -ENOMEM;
+	buf = malloc(cur_root->fs_info->csum_root->sectorsize);
+	if (!buf) {
+		ret = -ENOMEM;
+		goto out;
+	}
+
+	key.objectid = 0;
+	key.offset = 0;
+	key.type = 0;
+
+	ret = btrfs_search_slot(NULL, cur_root, &key, path, 0, 0);
+	if (ret < 0)
+		goto out;
+	/* Iterate all regular file extents and fill its csum */
+	while (1) {
+		btrfs_item_key_to_cpu(path->nodes[0], &key, path->slots[0]);
+
+		if (key.type != BTRFS_EXTENT_DATA_KEY)
+			goto next;
+		node = path->nodes[0];
+		slot = path->slots[0];
+		fi = btrfs_item_ptr(node, slot, struct btrfs_file_extent_item);
+		if (btrfs_file_extent_type(node, fi) != BTRFS_FILE_EXTENT_REG)
+			goto next;
+		start = btrfs_file_extent_disk_bytenr(node, fi);
+		len = btrfs_file_extent_disk_num_bytes(node, fi);
+
+		ret = populate_csum(trans, csum_root, buf, start, len);
+		if (ret == -EEXIST)
+			ret = 0;
+		if (ret < 0)
+			goto out;
+next:
+		/*
+		 * TODO: if next leaf is corrupted, jump to nearest next valid
+		 * leaf.
+		 */
+		ret = btrfs_next_item(cur_root, path);
+		if (ret < 0)
+			goto out;
+		if (ret > 0) {
+			ret = 0;
+			goto out;
+		}
+	}
+
+out:
+	btrfs_free_path(path);
+	free(buf);
+	return ret;
+}
+
+static int fill_csum_tree_from_fs(struct btrfs_trans_handle *trans,
+				  struct btrfs_root *csum_root)
+{
+	struct btrfs_fs_info *fs_info = csum_root->fs_info;
+	struct btrfs_path *path;
+	struct btrfs_root *tree_root = fs_info->tree_root;
+	struct btrfs_root *cur_root;
+	struct extent_buffer *node;
+	struct btrfs_key key;
+	int slot = 0;
+	int ret = 0;
+
+	path = btrfs_alloc_path();
+	if (!path)
+		return -ENOMEM;
+
+	key.objectid = BTRFS_FS_TREE_OBJECTID;
+	key.offset = 0;
+	key.type = BTRFS_ROOT_ITEM_KEY;
+
+	ret = btrfs_search_slot(NULL, tree_root, &key, path, 0, 0);
+	if (ret < 0)
+		goto out;
+	if (ret > 0) {
+		ret = -ENOENT;
+		goto out;
+	}
+
+	while (1) {
+		node = path->nodes[0];
+		slot = path->slots[0];
+		btrfs_item_key_to_cpu(node, &key, slot);
+		if (key.objectid > BTRFS_LAST_FREE_OBJECTID)
+			goto out;
+		if (key.type != BTRFS_ROOT_ITEM_KEY)
+			goto next;
+		if (!is_fstree(key.objectid))
+			goto next;
+		key.offset = (u64)-1;
+
+		cur_root = btrfs_read_fs_root(fs_info, &key);
+		if (IS_ERR(cur_root) || !cur_root) {
+			fprintf(stderr, "Fail to read fs/subvol tree: %lld\n",
+				key.objectid);
+			goto out;
+		}
+		ret = fill_csum_tree_from_one_fs_root(trans, csum_root,
+				cur_root);
+		if (ret < 0)
+			goto out;
+next:
+		ret = btrfs_next_item(tree_root, path);
+		if (ret > 0) {
+			ret = 0;
+			goto out;
+		}
+		if (ret < 0)
+			goto out;
+	}
+
+out:
+	btrfs_free_path(path);
+	return ret;
+}
+
+static int fill_csum_tree_from_extent(struct btrfs_trans_handle *trans,
+				      struct btrfs_root *csum_root)
 {
 	struct btrfs_root *extent_root = csum_root->fs_info->extent_root;
 	struct btrfs_path *path;
@@ -8691,6 +8825,23 @@ static int fill_csum_tree(struct btrfs_trans_handle *trans,
 	return ret;
 }
 
+/*
+ * Recalculate the csum and put it into the csum tree.
+ *
+ * Extent tree init will wipe out all the extent info, so in that case, we
+ * can't depend on extent tree, but use fs tree.  If search_fs_tree is set, we
+ * will use fs/subvol trees to init the csum tree.
+ */
+static int fill_csum_tree(struct btrfs_trans_handle *trans,
+			  struct btrfs_root *csum_root,
+			  int search_fs_tree)
+{
+	if (search_fs_tree)
+		return fill_csum_tree_from_fs(trans, csum_root);
+	else
+		return fill_csum_tree_from_extent(trans, csum_root);
+}
+
 struct root_item_info {
 	/* level of the root */
 	u8 level;
@@ -9250,7 +9401,8 @@ int cmd_check(int argc, char **argv)
 				goto close_out;
 			}
 
-			ret = fill_csum_tree(trans, info->csum_root);
+			ret = fill_csum_tree(trans, info->csum_root,
+					     init_extent_tree);
 			if (ret) {
 				fprintf(stderr, "crc refilling failed\n");
 				return -EIO;