This paper addresses the requirements for high-reliability, autonomy, and intelligence in high-performance unmanned aerial vehicles (UAVs) by introducing four typical emergency power system architectures, and proposing a new lithium battery—Ram Air Turbine (RAT) architecture. Based on identified needs such as reliable perception of the emergency power system, power connection time, prolonged operation, effects on formation stealth, and weight requirements, the study advances the architectural and logical design for energy autonomous operation control capabilities. Finally, autonomous operation control technologies for UAVs combat are proposed. The effectiveness of the system architecture and autonomous operation design is verified through digital simulation analyses under typical training and combat flight profiles. The simulation results demonstrate that the emergency power system architecture and autonomous operation control technology proposed in this paper have the characteristics of high reliability, autonomy, and robustness, which are critically important for enhancing the safety of emergency power in high-performance UAVs.