An analytical method of coarse alignment in flight based on quaternion which can be used in landing system was presented without any restrictive condition of dynamic process and flight stability. The formula of the coarse alignment which can solve the attitude of the airplane with the velocity measured by GNSS and specific force measured by inertial measurement unit were derived. The factors affecting the alignment performance were analyzed. The simulation results show that the method can be carried out in wide dynamic range with high accuracy, high speed and low computer complexity and can satisfy the requirement of speed and .precision of flight coarse alignment.