In order to estimate the misalignment angle of align system effectively, this paper constructs a traditional 14 state rapid transfer alignment model, considers the problem that traditional velocity error definition is not completely accord with the consistency of coordinate system, the improved differential equation of velocity error is applied to transfer alignment, constructs an improved 12 state rapid transfer alignment model. Finally, the performance of the two alignment algorithms is tested by vehicle-mounted experimental data under the conditions of no maneuver, C shape maneuver and S shape maneuver, and the experimental result of the two algorithms is compared and analyzed. The experimental result shows that the improved 12 state rapid transfer alignment algorithm not only has better alignment accuracy than the traditional 14 state rapid transfer alignment algorithm, but also reduces the model complexity, reduces the system calculation, and avoids the influence of flexural deflection and dynamic misalignment angle. The yaw angle alignment accuracy is improved by 45%, 65% and 53% under the conditions of no maneuver, C shape maneuver and S shape maneuver, respectively.