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Self-alignment of strapdown inertial navigation systems incorporating micro-electro-mechanical systems (MSINS) is a great challenge for marine applications. In this paper, a self-alignment method for a rotating MEMS strapdown compass is proposed with the aim of solving this problem. First, based on an analysis of biaxial rotation modulation and initial alignment of the strapdown compass, a self-alignment method is presented and verified. Second, by analyzing the effects of biaxial rotation modulation, the proposed method is improved by speeding up the rotation and reducing the stop time of the biaxial rotation mechanism to shorten the initial alignment time, which effectively suppresses the influence of MEMS noise on the initial alignment error angle. The influence of ship swinging on the initial alignment error angle is also analyzed. The efficiency of the method is verified by experiments on a swinging base. Finally, a parameter adjustment approach is presented that allows the proposed method to be used with different types of MEMS. This approach is validated by experiments. All the experimental results demonstrate the efficiency and precision of the proposed method.