A method of handling a multimedia broadcast multicast service (MBMS) minimization of driver test (MDT) for a network of a wireless communication system includes transmitting a first MBMS measurement configuration to instruct a first user equipment (UE) to perform an MBMS MDT operation; receiving a first MBMS measurement result and a first multicast-broadcast single frequency network (MBSFN) area identity (ID) which indicates that the first MBMS measurement result is generated for a first MBSFN area identified by the first MBSFN area ID, from the first UE; and processing the first MBMS measurement result according to the first MBSFN area ID.