To enhance the fuel efficiency of fuel cell hybrid electric vehicles (FCHEVs), we propose a hierarchical energy management strategy (HEMS) to efficiently allocate power to a hybrid system comprising a fuel cell and a battery. Firstly, the upper-layer supervisor employs a fuzzy fault-tolerant control and prediction strategy for the battery and fuel cell management system, ensuring vehicle stability and maintaining a healthy state of charge for both the battery and fuel cell, even during faults. Secondly, in the lower layer, dynamic programming and Pontryagin’s minimum principle are utilized to distribute the necessary power between the fuel cell system and the battery. This layer also incorporates an optimized proportional-integral controller for precise tracking of vehicle subsystem set-points. Finally, we compare the economic and dynamic performance of the vehicle using HEMS with other strategies, such as the equivalent consumption minimization strategy and fuzzy logic control strategy. Simulation results demonstrate that HEMS reduces hydrogen consumption and enhances overall vehicle energy efficiency across all operating conditions, indicating superior economic performance. Additionally, the dynamic performance of the vehicle shows significant improvement.