A method of handling an interference measurement for a communication device in a time-division duplexing (TDD) system comprises receiving a signal; measuring an interference coming from at least one cell with at least one uplink/downlink (UL/DL) configuration in the TDD system in a subframe according to the signal, to obtain a measured interference; and generating a measurement result comprising the measured interference and information of the at least one UL/DL configuration of the at least one cell.