A charge-controlling system and a method therefor are applicable to a backup power system having a fuel-cell-based power supply and a battery. The charge-controlling system includes a bidirectional converter, a feedback circuit, a voltage controller, a PWM generator, a switch unit and an over-charging protection circuit. The feedback circuit generates a feedback signal corresponding to an output voltage of the bidirectional converter. The voltage controller generates a control voltage according to the feedback signal and a constant voltage, such that the PWM generator generates a PWM signal based on the control voltage. The over-charging protection circuit controls operation of the switch unit according to the feedback signal and a saturation voltage of the battery. When the switch unit electrically connects the bidirectional converter and the PWM generator, the bidirectional converter charges the battery with the power generated by the fuel-cell-based power supply according to the PWM signal.