A battery charging system for a vehicle includes a generator, a battery, a DC/DC converter converting the electrical power generated by the generator and supplying the converted electrical power to the electrical device of the vehicle and supplying the electrical power to an electrical device, and charging the battery, an energy storage device storing the electrical power generated from the generator and providing the stored electrical power to the DC/DC converter, and an engine control unit controlling the generator to charge the energy storage device by providing regenerative power generated by the generator in a deceleration driving section of the vehicle, calculating a low-voltage control amount determined to correspond to a state of the battery connected to the DC/DC converter and whether the electrical device of the vehicle operates, and controlling the DC/DC converter to charge the electrical power in the battery based on the calculated low-voltage control amount.