As a high precision attitude measuring instrument in arc-second level, star sensor has become a necessary component for satellites, spacecraft and space station. However, star sensor misalignment angle can reach the arc-minute level and reduce the accuracy of the star sensor’s output severely. Since it’s difficult to measure the initial alignment error precisely on the ground, research applicable to star sensor misalignment angle calibration technique is necessary. To make the system get a high precision attitude control, a GPS-assisted Kalman filter modeling of the system was carried out. Finally, the misalignment angle from the board axes to the star sensor axes can be estimated by employing the derived relationship. The mathematical simulation results show the effectiveness of the calibration algorithm.