A method of handling a communication operation for a communication device configured with a first cell comprises the steps of performing a first communication operation in a subframe via the first cell, if a direction of the subframe determined according to a uplink (UL)/downlink (DL) configuration of the first cell and a direction of the subframe determined according to a reference UL/DL configuration are the same; and stopping the first communication operation in the subframe via the first cell, if the direction of the subframe determined according to the UL/DL configuration of the first cell and the direction of the subframe determined according to the reference UL/DL configuration are the different.