System and method for managing copy-on-write (COW) B tree structures for metadata of storage objects stored in a storage system determine, when a request to modify a target storage object stored in the storage system that requires a modification of a target leaf node in a B tree structure for metadata of the target storage object is received, whether an operation sequence number of the target leaf node is greater than a snapshot sequence number of a parent snapshot of a running point of the B tree structure. When the operation sequence number is greater than the snapshot sequence number, the target leaf mode is modified in place without copying the target leaf node. When the operation sequence number is not greater than the snapshot sequence number, the target leaf node is copied as a new leaf node for the B tree structure and the new leaf node is modified.