Aiming at the traditional multi-stack fuel cell system (MFCS) energy management strategy that cannot solve the problems of low efficiency and poor stability under complex operating conditions, an electro-hydrogen coupling coordinated and optimized control strategy taking into account the power allocation of the multi-stack fuel cell is proposed. In the state machine control layer, a fuel cell power allocation method is proposed to optimize the operating efficiency of the fuel cell, reduce the operating time of the fuel cell in the light load interval, and consider the residual power of the system, the state of charge (SOC) of the lithium battery, and the state of hydrogen (SOH) of the hydrogen storage tank to classify the operating states and reduce the operating time of each fuel cell in the system, so as to reduce the operating time of the fuel cell in the light load interval. The state is divided to reduce the number of switching times of the control modes of each device in the system and improve the service life and operational stability of the system; at the device control layer, the operation modes of each device are changed according to the control signals sent by the state machine to maintain the power balance of the system and smooth out the fluctuations of the DC bus voltage. Based on Simulink platform simulation, the results verify the rationality of the proposed control strategy.