Abstract: Magnetic flied vector is a function of the satellite's position.Autonomous LEO satellite navigation can be achieved based on the measurement data are of the onboard three axis magnetometer(TAM).But when measurement data influenced by outliers,filtering convergence velocity becomes slow and the filter even diverges. In this paper,based on residual orthogonal EKF fault tolerant filtering method,the instant modifying and fault diagnosis of the wild data are implemented and the filter possesses good robustness.Simulation results show the effectiveness of the method.