Due to technical limitations, it is difficult for single stack fuel cell (FC) system to be applied in high-power applications. Therefore, multi-stack FC hybrid system (MS-FCHS) is attracting more and more attention. In order to improve the system economy, this work proposes a real-time energy management strategy (EMS) that minimizes system operating cost. Specifically, the proposed strategy considers not only fuel cost but also FC and battery degradation cost. Secondly, during the operation of MS-FCHS, the performance of each stack varies with operating conditions and time, this work also considers the impact of inconsistent FC performance on the system lifetime. Finally, compared with the power following strategy (PF) and the hydrogen consumption minimizing strategy (H2-minimization), RT-LAB experimental results show that the proposed strategy can reduce the system operating cost by 15.85% and 9.75%, and improve system efficiency. In addition, since the system life depends on the stack with the worst service performance, the proposed strategy can also realize the convergent control of the system performance when the stacks operate in parallel, prolong the life of the system, and maintain battery state of charge (SOC) within a certain range, which is conducive to the stable operation of the system.