The Queqiao-2 satellite is a crucial part of the fourth Lunar Exploration Program mission. Compared to the Chang’e 4 Queqiao satellite, the Queqiao-2 satellite orbit changes from a Halo orbit at the Earth-Moon Lagrange L2 point to a circumlunar large elliptical orbit, with large changes in both relay communication and science load equipment. In this paper, the variation of solar heat flow and lunar infrared in a circumlunar large elliptical orbit with orbit is analyzed, which provides a basis for the design of the thermal control system of the Queqiao-2 satellite. In order to meet the temperature control requirements of the Queqiao-2 satellite in multi-mission mode and orbital attitude constraints, the thermal control system adopts a design scheme with adjustable heat dissipation capability based on loop heat pipe technology, while the design carries a positive temperature coefficient (PTC) self-controlled temperature heater, which is successfully applied in orbit. After Queqiao-2 was launched into orbit, the level of equipment temperature control during each flight phase was good. The first human lunar dorsal sample relay communications mission was substantially ensured by controlling the temperature of high-power relay loads, such as the Queqiao-2 X-band solid state amplifier, between 22 °C and 28 °C during the Chang’e 6 mission. The design method in this paper can provide a reference for the design of the highly adaptable thermal control system of a deep space exploration mission.