Abstract: The net output power of the proton exchange membrane fuel cell (PEMFC) system and the oxygen excess ratio (OER) have the characteristics of non-linearity and strong coupling. Therefore, the oxygen excess ratio hierarchical control method was proposed in this paper. The method was used to optimize and control the oxygen excess ratio of PEMFC system. The upper control was based on the offline+online oxygen excess ratio optimization algorithm. Feedback control based on super-twisting algorithm was used as the lower control. The super-twisting algorithm was used to replace the traditional PID feedback control. The Lyapunov function was used to prove the stability of closed loop system under sliding mode control. RT-LAB real-time simulation platform was built to carry out real-time simulation of PEMFC system. According to the real-time change of the net power of the PEMFC system, the results show that the proposed control method can automatically perform optimal control of the oxygen excess ratio. In the case of dynamic changes of the load current, the method meets the performance index requirements of the maximum net power and improves the efficiency of the system.