A power supply system for EV and a control method thereof are provided, the system including a high voltage battery generating a driving voltage to a motor of the EV, a low voltage battery generating a driving voltage for other electronic equipment, an LDC (low voltage DC-DC Converter) converting a high voltage generated by the high voltage battery to a low voltage, and generating a control power for charging the low voltage battery, an alternator generating a control power for charging the low voltage battery using a rotary power of the motor, and a control power selector selectively supplying the control power generated by the LDC or the alternator to the low voltage battery.