In hybrid power source system (HPSS) of more electric aircraft (MEA), energy management strategy (EMS) distributes power of each power source and single-objective optimization or multi-objective optimization can be realized. A double-layered (DOL) energy management strategy which is composed of fuzzy control layer for lithium battery and variable power reference filter layer for fuel cell system is proposed in this paper. The first layer is the fuzzy control layer which adds the extra input power reference of fuel cell, and it is related to efficiency of fuel cell system and state of charge of lithium battery. Second layer possesses a variable parameter which can keep the power reference of fuel cell close to the highest efficiency point and it has a good effect on the health and efficiency of fuel cell. By combining two layers, both SOC of lithium battery and efficiency of fuel cell system are regarded as the optimization objectives. For verifying proposed EMS, it is compared with finite state machine (FSM) energy management strategy and the simulation results shows that proposed EMS outdoes FSM EMS. In 50% initial SOC condition, average efficiency of fuel cell system and equivalent hydrogen consumption of the proposed EMS are 2.13% higher and 1.7 g lower than FSM respectively, and they are 1.84% higher and 1.5 g lower than FSM in 80% initial SOC condition. In addition, the proposed EMS is a real-time approach without demand of much calculation resource.