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The extremely low temperature in Antarctic inland area has taken a new challenge for telescope design and develop, the adaptability of components and parts in telescope for the environment close to space. The application of high accuracy encoder is the only way to improve the accuracy of tracking, however, due to the temperature requirement, there is no application of encoder under such a low temperature ever since. To realize the high accuracy of tracking and steering in telescope, high accuracy encoders must be applied in it. Based on the analysis of influence on encoder caused by temperature, an initial thermal control measure is carried out. Secondly, the thermal control measure is optimized with the method that consists of CFD simulations and experiments. Finally, an effective thermal control measure is applied on the second telescope of the 3 Antarctic Schmidt Telescopes (AST3). By the comparison of normal temperature experiment and low temperature experiment, the encoder can reach a temperature of about 25 degrees when it is under the circumstance of-80 degrees after the thermal control works, and the power consumes by the thermal control is less than 6W. The experiment result indicates that the thermal control measure can fit the requirement of temperature that ranges from-10 degrees to 80 degrees and the lowly consuming power requirement, the encoder can reliably work in low temperature with the thermal control measure works.