Concerning the fuel cell electric vehicles, the multi-stack fuel cell system (MFCS) offers superior performance and reliability over single stack fuel cell system. In order to obtain the lowest hydrogen consumption, this paper proposes a power allocation strategy using the Particle Swarm Optimization (PSO) algorithm. The MFCS is composed of two 300 W fuel cell stacks and a 360 Wh battery. The simulation results have shown that the performance of the proposed strategy can achieve more satisfactory results in terms of minimizing hydrogen consumption and managing the battery state of charge, compared to the equidistributional method.