Geomagnetic navigation is a new branch of the passive autonomous navigation technique. The theory of geomagnetic navigation was analyzed. The process of typical magnetic storm is described. The feasibility of geomagnetic navigation during magnetic storms is analyzed in this paper. With employment of experimental data, the measurement equations are obtained by using surface Spline method. Extended Kalman Filter (EKF) is applied to navigation calculation, and the navigation accuracy is discussed during different phases of magnetic storm. The simulations are calculated with theoretical model data and real magnetic storm data. Results show that the feasibility of magnetic navigation is verified during the initial and later recovery phases of all the storms. And the conclusion is also valid in all the phases of a storm which is less than or equal to moderate intensity. Positioning error is lower than 200 m, which meets the guidance requirement in the mid-course of flight vehicle.