The current new type of inertial navigation system, including rotating inertial navigation systems and three-autonomy inertial navigation systems, has been increasingly widely applied. Benefited by the rotating mechanisms of these inertial navigation systems, alignment accuracy can be significantly enhanced by implementing IMU (Inertial Measurement Unit) rotation during the alignment process. The principle of suppressing initial alignment errors using rotational modulation technology was investigated, and the impact of various component error terms on alignment accuracy of IMU during rotation was analyzed. A corresponding error suppression scheme was designed to overcome the shortcoming of the significant scale factor error of fiber optic gyroscopes, and the research content of this paper is validated through corresponding simulations and experiments. The results indicate that the designed alignment scheme can effectively suppress the gyro scale factor error introduced by angular motion and improve alignment accuracy.