A portable electronic device based user-definable remote-control interface system and operating method thereof is disclosed. The system integrates remote control information of a variety of remotely controllable devices into one single interface allocation information map, which is stored in and can be shown on a portable electronic device. To operate the user-definable remote-control interface, first show the interface allocation information map on the portable electronic device and define at least an object and a button in the map. Then, search a network platform for a built-in remote-control code that corresponds to the button, or receive a learning signal from a remote controller of a device to be remotely controlled with the button to generate a learnt remote-control code corresponding to the button. Finally, store the built-in or the learnt remote-control code in a storage unit of the portable electronic device and relate the remote-control code to its corresponding button.