In order to shorten the waiting time before experiment, reduce the damage caused by heat radiation and lower the influence of thermal deformation on the experiment, thermo-mechanical analysis of deflection focus system is carried out by making full use of synchrotron radiation X-ray to obtain stable and effective experimental results. Based on the main parameters of Shanghai synchrotron radiation facility (SSRF), the thermal power density distribution absorbed by deflection focus system on X-ray interference lithography (XIL) line is calculated. Then dynamic thermal equilibrium analysis is carried out under the conditions: without water cooling, with water cooling and thermal radiation. Finite element analysis is used to perform the thermo-mechanical analysis of M1, M2 in order to obtain parameters such as the time required for thermal equilibrium and the temperature gradient distribution. Results indicate that the thermal load effect on M1, M2 of deflection focus system can be weakened by indirect water cooling structure. Thermal equilibrium durations of M1, M2 get dropped substantially from 8677 s and 7850 s to 960 s and 840 s, respectively. The highest temperatures reduce from 182.73 ℃, 129.73 ℃ to 57.94 ℃, 47.29 ℃, respectively. Meanwhile, the biggest slope errors are 7.23 μrad, 9.24 μrad, respectively. The waiting time from operating to experiment is shortened, which can improve the efficiency greatly and ensure steady and effective experimental results.