A portable electronic system and power management method thereof are disclosed. The portable electronic system includes a portable host and a portable power supply. The portable host has a main battery and a connecting interface. The portable power supply has a backup battery, and is coupled to the portable host through the connecting interface, and transceives a work state of the portable host and the portable power supply and a system power provided by the portable host through the connecting interface. The portable host and the portable power supply control charge or discharge states of the main battery and the backup battery according to the work state. The work state includes relative state of charges (RSOC) of the main and backup battery and information of whether the portable host is coupled to a power adaptor for receiving an external power.