According to the thermal design of the Active Phased Array Antenna(APAA),base on the state of thermal control technology with the APAA and the multiphysics theory, this paper use CAD/CAE and thermal-structural integrated analysis method to probe into structural-electrical-thermal multiphysics analysis method with APAA. This paper elaborate a new method of the fluid-thermal-structural coupling analysis with APAA. base on the theory of the fluid-thermal coupling analysis and thermal-structure coupling analysis. The paper make a numerical model of APAA, a good thermal design is made to this model, it make the APAA work well. The conjugate heat transfer was made as fluid and solid interface boundary condition, the proper discretization and SIMPLE algorithm is chose in fluid-thermal coupling analysis by using FLUENT software. The temperature of the APAA is got. The important parameters which influent the temperature of the APAA is listed. Comput the distortion of the APAA in the condition of different temperature,restriction and temperature grads. The important parameters which influent the distortion of the APAA is listed, the electrical parameters is also computed in the condition of different distortion with APAA, got some conclusion which influent the electrical parameters of APAA. The paper provide valuable guidance to improving the thermal control and the electrical performance of the APAA.