The KDUST telescope would be installed in Antarctic Dome A, where is extremely cold, high, dry, but have a very stable, calm atmosphere for astronomical observation. According to project requirement, the position following error should be less than 1‘’. To achieve project target, a direct drive method is used in the project. Normal PID control algorithm is used in controller. It can meet the target in the room temperature. But the following error increased too significantly in the cryogenic environment. In this paper, the expert PID algorithm is applied to control system. The control parameter can be adjusted by amplitude and variation of following error. Experiment proved that expert PID has an obvious advantage in both start-up and tracking process under different temperature. Moreover expert PID also can improve the stability of whole system.