The influence of aerothermoelastic dynamic response on the performance of the three-dimensional hypersonic inlet is investigated in this paper. A dynamic aerothermoelastic analysis framework is developed. The reliability of the framework is verified. The effects of aerodynamic heating on the dynamic response, the effects of the aerothermoelastic dynamic response of the inlet on the flow field structure, and the performance parameters are studied. The results indicate that the static deformation of the leading edge structure is large while the vibration amplitude is small. Meanwhile, the vibration amplitude of the trailing edge structure is larger. The aerothermoelastic dynamic response changes the shock wave structure near the exit, strengthens the shock wave intensity, increases the length of the separated region, and changes the flow field of the exit. Simultaneously, the flow field structure also experiences obvious dynamic changes at different moments. The dynamic response increases the time-averaged flow coefficient, reduces the time-averaged total pressure recovery coefficient, and improves the time-averaged reverse pressure ratio. At the same time, the dynamic response leads to the fluctuation of performance parameters, especially the large fluctuation range of the reverse pressure ratio at the exit.