Due to the features of complicated test environment, variable parameters, and limited conditions in real car experiment, it has proposed a Hardware-in-Loop test platform for Fuel Cell System (Short for FCS) based on hardware of NI PXI and software of NI Labview to fuel cell vehicle. According to FCS’s control strategy, I/O signal map, CAN communication and sensor characteristics, it has designed the hardware configuration, software program, test interface, and rapidly made validation to control logic and fault diagnosis of Fuel Cell System’s Electronic Control Unit (Short for FCU). The experiment result shows that this test platform is effective for FCU control logic validation, system status monitor, fault injection, fault tracing, and it can shorten the vehicle research and development cycle, reduce the development cost, optimize test environment and promise safety for test engineer. This test platform will make good effect to vehicle electrical system development and supply reference for vehicle test.