A communication device for handling a temporary UE configuration comprises a storage device for storing instructions and a processing circuit coupled to the storage device. The processing circuit is configured to execute the instructions stored in the storage device. The instructions comprise receiving a configuration from a first base station; communicating with the first BS according to the configuration; transmitting a first message to the first BS to request changing the configuration; performing a handover to a second BS; and transmitting the first message to the second BS to request changing the configuration, when connecting to the second BS in response to the handover.