In complex flight conditions, due to the large amount of unusable heat generated by aerodynamic heating, the thermal protection system of an aircraft needs to withstand a large temperature shock, which brings great challenges to the design of the structure. In order to effectively utilize the irregular aerodynamic heat, and improve structural heat conduction, a composite structure is formed by using phase change energy storage materials on the basis of the thermoelectric structure, which transforms the aerodynamic waste heat into stable electric energy for the internal system. Through the study of the response of nonlinear transient energy, it is found that the thermoelectric and mechanical properties of the new structure can be improved by adding phase change energy storage materials. Under actual flight conditions, the new structure can reduce the maximum temperature by 180 K and the maximum thermal stress by 110 Mpa. The mechanical properties of the structure are effectively improved, the service life of the structure is prolonged, and the waste heat can be converted into stable electrical energy output to improve the thermoelectric output performance. On the premise of ensuring conversion efficiency, the output power of the new structure has been improved by 64.8% through structural optimization under actual flight conditions.