The purpose of this paper is to tackle the problem of cost and efficiency brought by DC/DC to the fuel cell vehicle drive system. The energy transfer between dual power sources and the independent control of the corresponding torque are also expected to be realized. The operating mode, control system, and output performance of the dual-power source motor drive system were analyzed. Firstly, the models of the dual-power source electric motor, the fuel cell, and the power battery were developed. The multiple operating modes of the dual-power source electric motor were discussed. Then, considering the coupling effect between voltage of the two sets of windings in dual-power source motor, the feed-forward compensation combined zero direct-axis current strategy was adopted to control the winding current and corresponding torque individually. Finally, bench tests under laboratory-designed operating condition and basic urban drive cycle were conducted respectively. The output torque of the dual-power source electric motor drive system could quickly respond to the torque demand. The fuel cell and power battery winding currents in different operating modes were consistent with their corresponding torque waveforms. The bench test results showed that the multiple operating modes of the dual-power source electric motor drive system could realize the starting, acceleration, downhill, and braking energy recovery conditions of the fuel cell vehicle. The adopted control strategy could realize the independent control of the output torque corresponding to the fuel cell and power battery, and the energy transfer between the fuel cell and power battery.