A communication control system applicable to a portable communication apparatus and a method thereof are disclosed. The communication control system includes a first communication module, a second communication module, a detector, and a controller. A first wireless signal is sent and received between the first communication module and a first base station via a first communication network. A second wireless signal is sent and received between the second communication module and a second base station via a second communication network. The detector detects the statuses of the first communication module and the second communication module. If one of the communication modules is detected being in communication, the detector triggers the controller to stop the other communication module from using the corresponding communication network.