Airborne multispectral scanners usually use large diameter planar blackbodies as their thermal reference sources. Because of the wide temperature range in air environment and the fact that the surface of a planar blackbody is susceptible to air flow, it is difficult to control the temperature of a large diameter planar blackbody accurately when designing an airborne multispectral scanner. A new temperature control system for planar blackbodies is designed. The system firstly uses an embedded PID algorithm based on CompactRIO to generate PWM signals and then uses the PWM signals amplified via an H bridge to control the heating and cooling of a thermopile. The experimental result shows that in air environment, the control system can adjust the temperature of a planar blackbody to the range of 20℃ of the ambient temperature with a control accuracy of 1℃. It can meet the application requirement of a thermal infrared source.