The present invention discloses a battery charging controller for balancing the charged batteries. The battery charging controller comprises a battery reference voltage generator, a voltage balancing module and a balance judging circuit. The battery charging controller determines which one has the lower voltage between battery units of a battery module according to reference voltages generated by the battery reference voltage generator. The voltage balancing module controlled by the balance judging circuit allows the charging current of the lower-voltage battery larger than the charging current of the higher-voltage battery in such that the final voltages of the battery units are substantially equaled when they are completely saturated.