The conventional alignment method cannot be applied to the vehicle navigation due to the low performance of IMU, which causes the problem of large heading uncertain alignment. In this paper, two trigonometric functions of the heading uncertain angle are used as the quantity of state to establish the a new linear system equation. On the other hand, the coarse and fine alignment procedures are unified to avoid the covariance information loss during the switching from the coarse alignment to the fine alignment. The vehicle test results verified the heading error of the new alignment method can be lower than 1°.