A reasonable energy management strategy (EMS) for a hybrid power system can effectively optimize the critical indicators of the system. In this paper, a Multi-level EMS that can improve the energy utilization rate of the fuel cell hybrid electric vehicle (FCHEV) was proposed. Focused on the energy distribution, a system overall efficiency optimization model was built first. Then, to reduce the computational burden caused by solving the optimization model, an instantaneous optimal search (IOS) algorithm with better online performance was proposed. Thus, the corresponding load demand power distribution strategy that can optimize the system overall efficiency can be designed. Hardware in the loop (HiL) experimental results indicated that the proposed EMS can realize optimization of the FCHEV energy utilization rate compared with other traditional strategies. To further validate that the proposed strategy can contribute to the practical application of the fuel cell electric vehicle, a 1.2kW hybrid electric vehicle was built in the laboratory. Results of the vehicle driving tests indicated that the designed EMS can effectively optimize the overall efficiency of the FCHEV hybrid power system, which can help to contribute to the application of fuel cell hybrid electric vehicles.