A power conversion system for vehicles is provided. The system includes a first energy storage device and a charging device with a rectification circuit for rectifying AC power to generate a DC link voltage. A DC-DC converter converts the level of the DC link voltage to generate a charging voltage of the first energy storage device. A low voltage DC-DC converter selectively down-converts one of the voltage of the first energy storage device and the DC link voltage to output a low voltage having a predetermined level. The low voltage DC-DC converter selectively converts one of the voltage of the first energy storage device and the DC link voltage into the low voltage based on whether the first energy storage device is charged according to input of the AC power.