In order to achieve more precise calculation result of navigation system error for maneuvering vehicle, the concept of 3D trajectory difference computing was introduced in this article, compared with the shortage of conventional algorithms that incorrectly simplified for flexible flight trajectory. Taking the lateral and normal apparent acceleration, roll and yaw angles into account, based on general error model of strap-down inertial navigation system, the hit accuracy can be acquired by numerical integration in which the right function deduced from gyroscope and accelerometer error item excited by trajectory parameters. The simulation result demonstrates that the algorithm compensates the disadvantage of oversimplification of previous method and highly improves calculation accuracy.