In recent years, the number of deep wells and ultra-deep wells is increasing gradually, and the bottom hole temperature of many wells reaches more than 200 °C, which puts forward higher requirement for the downhole measurement-while-drilling system. In this paper, a new active cooling method is proposed to protect electronic components in the electronic cavity from high temperature. The circuit board is cooled by direct contact with the cold end of a custom split-Stirling refrigerator. According to the different heat loads, the electronic components can operate in the proper temperature range by adjusting the piston motion frequency and inflation pressure. At the same time, the electronic cavity is filled with thermal insulation material to induce heat leakage from the environment. The thermal resistance of solid insulation material, argon, and vacuum is studied, and the required effective cooling power is determined. When the thermal insulation material is vacuum, which is the best resistance medium when compared with solid insulation material and argon according to the research results, the effects of the structure size of circuit board and electronic cavity, material property and operational environment on the required effective cooling power and maximum temperature on the room temperature chamber wall of the split-Stirling refrigerator are discussed.