The present invention provides an apparatus for controlling a capacitor charging circuit and a method thereof. The apparatus includes a first comparator, a second comparator, and a controller. The first comparator, which is coupled to the charging circuit, receives a voltage level and compares the voltage level with a reference voltage level to generate a first indication signal. The voltage level corresponds to an output voltage of the charging circuit. The second comparator receives a control value and compares the control value with a threshold value to generate a second indication signal. The controller, which is coupled to the charging circuit, the first comparator and the second comparator, generates a control signal according to the first indication signal and the second indication signal to turn the charging circuit on and off, and further generates the control value according to the control signal.