In order to ensure the normal operation of the star sensor during the on-orbit mission of the application platform, it needs to be thermally designed. First, a process of thermal analysis and optimization was proposed, which combined with the conditions of the external heat flow, installation layout and working mode of the micro star sensor assembly. In the process of thermal analysis optimization, the influence of various factors, such as optical, mechanical and thermal, was considered. Second, a thermal control scheme of the micro star sensor assembly was designed. The thermal control scheme proposed a design idea of using active electric heating and homogenizing the temperature between the light-shield and the star sensor body, which solved the problems of complex space thermal environment, higher temperature control requirements, and heat dissipation path limited by a installation structure during the on-orbit period of the micro star sensor module. This scheme ensured the effective and reliable work of the micro star sensor assembly. Third, an I-DEAS/TMG finite element mode was established. The thermal control simulation of the micro star sensor assembly under high and low temperature conditions was carried out, and the simulation results of the temperature distribution and uniformity of the star sensor assembly were analyzed. Finally, a ground test was carried out to ensure the correctness of the thermal control scheme, and the test results met the thermal requirement of the star sensor assembly. This paper can provide a reference for the following thermal design of micro star sensor assembly of on-orbit platforms.