In order to simplify the process and improve the accuracy of ship-borne star sensor install matrix calibration, a dynamic method which uses star sensor information and INS information to calculate install matrix is proposed. Theproposed method divides the calibration process into coarse calibration step and fine calibration step. Coarse calibration step calculates the coarse install matrix without consider the influence of atmospheric refraction. By using coarse install matrix and the atmospheric refraction compensation algorithm model, the atmospheric refraction is compensated and the accurate install matrix is calibrated in fine calibration step. Experiment results show that the proposed method can get the accurate calibration result by only two iterations and the install matrixes calibrated in different times are consistent. The contrastive results of star sensor attitude and INS attitude show the correctness of the proposed method.