Proton Exchange Membrane Fuel Cell (PEMFC) is difficult for application because of its high current and wide voltage output. A fractional order PID controller is introduced to a Four-Switch Buck-Boost DC/DC converter to stabilize the power output in this project. To reduce the inductor current ripple, a kind of dual-triggered switch strategy is employed in detail, and an accurate dynamic model of DC/DC converter is proposed for fuel cell measurement and control system. Then a fractional order PID controller is designed for voltage module compensation, in which a stochastic inertia weight PSO algorithm is employed to optimize the parameters of this controller. The results of simulation and experiment indicate that the compensation effect of fractional order PID controller has better performance than the integer order controller, which is robust to the variation of fuel cell system dynamics and power request.