A dual battery power management system, its battery controller and method for controlling the same have been provided. The dual battery power management system includes a load module, a battery controller, a first battery and a second battery. The battery controller is electrically connected to the load module for receiving an electrical requirement demanded by the load module. The battery controller is provided with a DC-DC converter and a serial-parallel switch. The first battery is employed to provide a first input voltage which is converted to a converted DC voltage by the DC-DC converter. The second battery is electrically connected to the serial-parallel switch and is used to provide a second input voltage. Upon the aforementioned electrical requirement, the battery controller controls the series-parallel switch to be operated at a serial mode or a parallel mode.