A balloon-borne telescope is a efficient planetary observation method by a telescope mounted on a balloon gondola in the stratosphere. In order to observe planets in high accuracy, the pointing control system to catch and keep the target star in the field of view of the mission camera is important technology. This research aims to develop the high accuracy pointing control system of the balloon -borne telescope. In case of conducting the pointing control divided into the gondola attitude control and the telescope pointing control, vibration of the gondola attitude caused by disturbance influences the accuracy of the telescope pointing control. It is expected that the performance of the telescope pointing control is able to be improved by a compensation controller to cancel the influence of the gondola attitude disturbance. In this paper, the pointing control system equipping with the attitude disturbance compensator is proposed, and verification by some simulation studies are described.