In order to achieve high-efficiency heat dissipation of a “stacked” time–frequency payload and high-precision high-stability temperature control of the payload upper module under complex space thermal environment, a two-stage thermal control system is proposed and established. In the first stage, the controllable heat dissipation path based on semiconductor thermoelectric coolers (TEC) along with microchannel vapor chamber (VC) is employed to build and control the thermal resistance between the upper module and the cold plate. In the second stage, the thin-film electric heater is used to carry out short-period PWM temperature control for the internal electronic components. The two-stage thermal control strategy realizes efficient heat dissipation of the upper module and ensures temperature stability of the internal point. To satisfy the high-precision and high-stability requirements, the thermal control system also features with on-orbit calibration and debugging capabilities, further improving the robustness of the system. In addition, this paper also analyzes the difference between ground test and on-orbit flight environment of key components of the system. Performance optimization is carried out according to on-orbit environment. Results show that the thermal control design is feasible, and the optimization methods for the difference of on-orbit environment are effective. Using the two-stage precision temperature control, the temperature fluctuation of all high-precision constraint points of the payload upper module precedes the requirements of ±0.1 ℃.