The safety and reliability of energy systems are the primary prerequisites for the long endurance stationary flight missions of unmanned aerial vehicles (UAVs) in near space. Firstly, the experimental platform of the energy system of UAVs in near space and its operating principle are introduced, and the typical faults in the energy system are analyzed. Then, the research progress of energy system fault diagnosis is described, and the effectiveness and shortcomings of existing methods are summarized. Finally, considering the actual requirements of the energy system of UAVs in near space, the issues and directions to be studied in the future are discussed.