Fuel cell/battery hybrid energy storage system (HESS) powered unmanned aerial vehicle (UAV) has the outstanding advantage of long endurance time. Trajectory tracking motion is a commonly used task execution mode of UAVs, especially in autonomous UAVs. This study aims at developing a control architecture to coordinate energy management with trajectory tracking control for fuel cell/battery hybrid UAVs. Its position tracking control adopts model predictive control (MPC) and an extended state observer to eliminate the modeling errors and effect of interference. The attitude tracking control adopts an auto-disturbance rejection controller having a quick response. The obtained control parameters are given as an input to the energy management block. Energy management strategies (EMSs) based on online dynamic programming and hierarchical MPC have been proposed. The results obtained from a simulation show that the proposed trajectory tracking control architecture can track the target trajectory stably with a small tracking error. The tracking performance is stable under interference. Experimental results show that dynamic programming is solved online with good control performance. Compared to ordinary EMSs, dynamic programming and hierarchical MPC can increase endurance time by 2.69% and 1.27%, respectively. The proposed control architecture verifies the coordination of energy management and trajectory tracking control, and prospected the advantages of the combination of fuel cell and autonomous driving for long endurance UAVs in the future.