With the development of high-altitude and long-endurance unmanned aerial vehicles (UAVs), optimization of the coordinated energy dispatch of UAVs’ energy management systems has become a key target in the research of electric UAVs. Several different energy management strategies are proposed herein for improving the overall efficiency and fuel economy of fuel cell/battery hybrid electric power systems (HEPS) of UAVs. A rule-based (RB) energy management strategy is designed as a baseline for comparison with other strategies. An energy management strategy (EMS) based on fuzzy logic (FL) for HEPS is presented. Compared with classical rule-based strategies, the fuzzy logic control has better robustness to power fluctuations in the UAV. However, the proposed FL strategy has an inherent defect: the optimization performances will be determined by the heuristic method and the past experiences of designers to a great extent rather than a specific cost function of the algorithm itself. Thus, the paper puts forward an improved fuzzy logic-based strategy that uses particle swarm optimization (PSO) to track the optimal thresholds of membership functions, and the equivalent hydrogen consumption minimization is considered as the objective function. Using a typical 30 min UAV mission profile, all the proposed EMS were verified by simulations and rapid controller prototype(RCP)experiments. Comprehensive comparisons and analysis are presented by evaluating hydrogen consumption, system efficiency and voltage bus stability. The results show that the PSO-FL algorithm can further improve fuel economy and achieve superior overall dynamic performance when controlling a UAV’s fuel-cell powertrain.