In view of the difficulty of initial alignment under the condition of large misalignment angle, a new initial alignment method of GPS/INS navigation system is proposed in this paper. Taking full advantage of the external information provided by GPS and using the error of the cosine function of the misalignment angle as the state variables, the effects of the GPS lever arm on the initial alignment are analyzed. On the basis of the above work, an improved filter compensation algorithm is proposed. The proposed method can not only compensate for the azimuth misalignment angle, but also can directly solve for navigation under the condition of the low precision of azimuth calculation, without waiting for the alignment process to be end. In the onvehicle test, the comparison between the new method and the traditional alignment method under the premise of small misalignment angle is carried out and the results are analyzed. The results show that this method can complete the alignment within about 100 s under the condition of large misalignment angle, the misalignment angle can converge within 1°, and the navigation position error can be controlled within 2 m.