A portable compound battery unit management system comprises a portable high capacity battery unit, a main power battery unit, and a DC converter. The portable high capacity battery unit has a built-in battery management means and is connected to the DC converter. The main power battery unit supplies power to a motor which in turn drives the vehicle, and contains another battery management means or a device for limiting maximum output current, or provides the DC converter and a motor controller installed behind with battery information required to operate the vehicle. The DC converter transfers the electrical energy of the portable high capacity battery unit to the main power battery unit, or converts output power of the portable high capacity battery unit to a necessary power required to operate the motor controller, wherein it has boost up or buck down function of voltage to match the voltage difference between the two battery units. With this scheme, the effectively combined portable high capacity battery unit and main power battery unit are very convenient to supply mechanical power for driving the motor bicycle to travel desired distance with a low operation and maintenance cost.