This paper presents the new in-flight alignment method using the flight distance of vehicle in order to improve the performance of the heading error estimation. In the proposed method, the Kalman filter having the difference between GPS and SDINS position as measurements is used for levelling of SDINS and heading error is estimated utilizing the flight distance information. It is shown in the simulation results that the in-flight method proposed in this paper has the high accuracy in heading error estimation and the heading error can be very quickly estimated at the high speed vehicle, compared with the existing method using the Kalman filter.