A communication device for handling a random access (RA) procedure comprises a storage unit for storing instructions and a processing circuit coupled to the storage unit. The processing circuit is configured to execute the instructions stored in the storage unit. The instructions comprise performing a first RA procedure to a base station according to a first RA configuration, if the communication device determines that a first condition is satisfied; and performing a second RA procedure to the base station according to a second RA configuration, if the communication device determines that a second condition is satisfied; wherein the first RA configuration corresponds to a first transmission time interval (TTI) length, the second RA configuration corresponds to a second TTI length, and the first TTI length is shorter than the second TTI length.