The multiple working modes, complex working conditions, frequent changes in external heat flux, and high power consumption of communication satellites all pose great difficulties to their thermal design. This paper mainly describes the design of a thermal control system for high-power communication satellites. Firstly, new efficient heat transfer technologies and thermal control materials for spacecraft are introduced. Secondly, the structure and internal heat source of the satellite are introduced. Thirdly, the external heat fluxes are analyzed, and the position of the heat dissipation surface and extreme conditions are confirmed. Then, a thermal control system is designed around the difficulties of thermal control. With heat pipes, the temperature uniformity of +Y deck, −Y deck, and +Z deck increased by 8 °C, 9.9 °C, and 34.2 °C, respectively. Furthermore, the maximum temperature of the power controller, secondary power supply, bidirectional frequency converter, and solid discharge decreased by 32.5 °C, 22.0 °C, 14.0 °C, and 164 °C, respectively. Finally, a thermal balance test is performed. The test results show that the temperatures of the solid-state power amplifier, on-board computer, power controller, secondary power supply, and bidirectional frequency converter meet the requirements of the thermal control indices. In addition, the temperature of thermal-sensitive components such as batteries and the storage tank also meets the requirements. The thermal design scheme is reasonable and feasible, and the thermal balance test verifies the correctness of the thermal design.