A fuel cell system includes a comparator, a signal tracking controller, a first load distribution controller, a first loop gain controller, a first adder, a first PWM controller, a first fuel cell and power converter, a second load distribution controller, a second loop gain controller, a second adder, a second PWM controller, and a second fuel cell and power converter. According to the proposed fuel cell parallel system, each fuel cell connected in parallel can have a different output voltage, but the voltage at the load side can be maintained. In addition, the power output ratio of each fuel cell can be controlled under the nominal load conditions and the load varied.