Abstract: The liquid crystal birefringent filter has become the preferred technology option for deep space magnetic field exploration missions due to the use of low-voltage actuators, removal of rotary motors, and other technical features, which greatly simplify the filter’s opto-mechanical structure. The refractive index of optical elements in filters is very sensitive to temperature changes. In order to ensure that the passband of the filter remains stable within a range of 0.1 ˚A, and meet the high sensitivity requirements for space magnetic field observation, it is necessary to achieve a temperature stability accuracy of ±0.005 ℃ within the optical cavity of the filter. Due to the low resolution of the available astronaut-grade Analog-to-Digital Converter (ADC), which are unable to meet the requirements for high-precision measurements if used directly, in this paper, we segmented the temperature range and designed the scheme of multi-stage amplification, low-pass filter circuit and space grade ADC to realize a wide range of temperature signal acquisition from −20 ◦C to 100 ℃ and a high resolution temperature acquisition of 0.0002 ℃ within the target temperature range of 38 ℃ to 46 ◦C. Then, the thermoelectric cooler (TEC) was used as the thermal control element with incremental PI (Proportional Integral) control algorithm, which realizes the precision temperature control, and the system temperature control accuracy was better than ±0.005 ℃ in the vacuum test. The above work can not only provide a precise temperature control system for ground-based liquid crystal birefringence filters, but also provide a feasible technical solution for deep space solar magnetic field and velocity field measurements.