A fuel cell system and a power management method thereof are provided. The fuel cell system includes a fuel cell power generation part, a switch circuit, a load supply circuit, a status detector, an electronic load circuit, and a control circuit. An input terminal and an output terminal of the switch circuit are respectively coupled to the power generation part and the load supply circuit. The status detector is coupled to a node between the power generation part and the input terminal to detect an output voltage of the power generation part. The electronic load circuit is coupled to a node between the power generation part and the input terminal to perform a current-sinking operation. The control circuit is for generating a first and a second control signals respectively for switching the on-off states of the switch circuit and controlling the current-sinking value of the electronic load circuit.