For the big error of commonly used earths main magnetic field model, a ship geomagnetic independent navigation system is designed by the rectangular harmonic model instead which describes the crustal anomaly field in the small-scale area. Motion equation of surface ship combined with the observation equation of rectangular harmonic model constitutes an independent navigation system. Meanwhile, in order to avoid the truncation error, the unscented Kalman filter algorithm is adopted. The simulation results show that the navigation system has a high accuracy. The position error is less than 2m. It can be used as an independent navigation.