Compared with conventional fuel aircraft or electric aircraft with a single battery source, the adoption of hybrid power in UAVs has become an increasingly popular research direction because it will reduce carbon emissions, reduce energy consumption or increase flight time.However, due to the complex operating conditions and drastic load changes of UAV, the power demand cannot be satisfied by fuel cell alone. It is necessary to add energy storage elements such as lithium battery or super capacitor as its auxiliary power supply. Therefore, the research on energy management strategy of hybrid power system with fuel cell as the main power supply is of great significance to solve the problem of UAV endurance time. Focusing on the UAV hybrid system based on fuel cell-lithium battery-supercapacitor, a model predictive control energy management strategy based on the minimum equivalent hydrogen consumption algorithm is proposed in this paper. The strategy applies the minimum equivalent hydrogen consumption strategy to the model predictive control framework, which not only meets the system load demand, but also improves the fuel economy. Finally, the simulation results show that the hydrogen consumption of the system is reduced effectively and the optimal power distribution is realized.