A security control system for improving security. The security control system includes a portable device, having a communication function and a portable device ID code. A security controller includes a memory for recording a controller ID code. The security controller communicates with the portable device and determines whether the portable device ID code matches the controller ID code. In accordance with the determination, the security controller selectively deactivates the security functions of a door lock driver and an engine controller. The security controller records and registers the portable device ID code as the controller ID code in the memory and transmits a registration signal containing the portable device ID code. A portable device management apparatus receives the registration signal from the security controller and manages the portable device based on the registration signal.