In previous research, a semi-strapdown inertial navigation system (SSINS), based on micro-electro-mechanical system (MEMS) sensors, was able to realize over-range measurement of the attitude information of high-rotation missiles by constructing a single axis “spin reduction” platform. However, the MEMS sensors in SSINS were corrupted by significant sensor errors. In order to further improve SSINS measurement accuracy, a rotational modulation technique has been introduced to compensate for sensor errors. The ideal modulation angular velocity is changed sharply to achieve a constant speed, while in practical applications, the angular rate of the rotating mechanism’s output needs to go through an acceleration-deceleration process. Furthermore, the stability of the modulation angular rate is difficult to achieve in a high-speed rotation environment. In this paper, a novel rotation scheme is proposed which can effectively suppress the residual error in the navigation coordinate system caused by the modulation angular rate error, including the acceleration-deceleration process and instability of angular rate. The experiment results show that the position and attitude accuracy of the new rotation scheme was increased by more than 56%. In addition, the proposed scheme is applicable to navigation accuracy improvement under various dynamic conditions.