A communication device of handling a measurement gap comprises a storage device and a processing circuit, coupled to the storage device. The storage device stores, and the processing circuit is configured to execute instructions of: connecting to a master base station (MBS); connecting to a secondary base station (SBS), while connecting to the MBS; receiving a first measurement gap configuration configuring a first plurality of measurement gaps for the communication device, from the SBS; determining a first plurality of locations of the first plurality of measurement gaps according to a first system time acquired from the SBS; and performing at least one first measurement on a first carrier in the first plurality of measurement gaps according to the first plurality of locations.