Abstract: In order to improve the overall efficiency of multi-stack fuel cell system (MFCS) and maintain the stability of the bus voltage, a MFCS efficiency optimal control method based on the Salp swarm algorithm (SSA) was proposed in this paper. The method optimized the overall efficiency of the system in real time through the fast search capability of SSA to realize the reasonable distribution of power among multiple fuel cells. Then, it maintained the long-term stability of the bus voltage through the droop control strategy. Finally, through the hardware-in-the-loop (HIL) simulation platform built on RT-LAB, the method was compared with the average power distribution method and the Daisy chain power distribution method. The experimental tests were conducted in terms of power, efficiency and fault tolerance. The results show that the SSA optimization algorithm and droop control strategy can ensure the real-time optimization of the overall efficiency of MFCS and stabilize the bus voltage.It can also enhance the fault tolerance of the system and reduce the operating cost of MFCS, which is beneficial to improve the durability and anti-disturbance ability of the fuel cell.