To meet the demand for high-precision temperature control of gravitational wave detection spacecraft, a research approach of precise temperature control driven by time-frequency analysis is presented in this paper. A multistage temperature control model based on the nested configuration of gravitational wave detection satellites is established, and the heat transfer characteristics and allocation methods within the system are clarified. On this basis, the multistage temperature control method based on PID is explored, and the numerical analysis results indicate that it can reach the sub-mK level and also achieve mK level stability in orbit tests. The results of frequency domain analysis reveal that noises of different frequency bands will be introduced into the temperature measurement and control system, and how to identify and effectively suppress these noises is the main research direction of precise temperature control for gravitational wave detection satellites.