In air supply subsystem , the stack pressure influence the stack efficiency as well as air compressor power consumption. In order to improve system global efficiency, the optimization of system efficiency based on the two inputs manipulation variables such as opening position of back pressure valve(BPV) and air compressor command voltage were investigated at a series of given system net power. Meanwhile, for a given fuel cell system, the BPV with the different diameters were adopted to match the system, and the simulations show that the BPV with the diameter of 30mm is good for the system with the purpose of the control accuracy.