The Taiji-1 satellite is a pioneering space technology mission designed by the Chinese Academy of Science (CAS) to test key technologies required for gravitational wave detection in space. Temperature stability is a critical element because it can couple with the gravitational wave measurement. A dedicated thermal control with a three-level control method was used on the Taiji-1 satellite science module. The simulation analysis shows that the temperature stability control level of its scientific instrument temperature stability can reach ± 1.7 mK. Combined with the in-orbit temperature results, the temperature stability obtained by using the linear smoothing filter and the Kalman filter reached ± 1.1 and ± 0.5 mK, respectively, which were in good concerted with the simulation data, indicating that the thermal control level of Taiji-1satellite science module reached a high precision.