The axis alignment test system is an important instrument for measuring the parallelism of optical axes by applying the method of large aperture parallel light tubes, with a focal length of 4800 mm and an aperture of 600 mm. During the test process, due to the long focal length and large aperture, the small deformation of each component caused by the change of the ambient temperature will affect the imaging quality of the system and the test accuracy. Therefore, an opto-mechanical thermal integration analysis of the system is required. The finite element analysis model of the shaft alignment test system was established, the thermal deformation of the system under steady state temperature field and temperature gradient field was analyzed, the Zernike polynomials were used to fit the surface shape of the mirror after thermal deformation, and the fitting coefficients were imported into the optical design software to get the effects on the shaft alignment test system under different temperature changes, and the accuracy of the simulation results was verified by experiments. The results show that: under the steady state temperature field, within the temperature range required by the design parameters, the wave aberration of the optical system is less than λ/10 (λ=632.8 nm), and the accuracy of the optical axis consistency detection meets 0.02mrad; the temperature gradient field has a greater impact on the system, and it is necessary to control the temperature difference between the inside and the outside of the system to within ±3℃.