Self-alignment of strapdown inertial navigation systems incorporating micro-electromechanical 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 selfalignment 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. INDEX TERMS Biaxial rotation modulation, MEMS, self-alignment, strapdown compass. WEIQUAN HUANG received the B.S. degree in underwater acoustic electronics from the Harbin Shipbuilding Engineering Institute, in 1989, and the M.S. degree in information and signal processing and the Ph.D. degree in control theory and control engineering from Harbin Engineering University, in 1994 and 2006, respectively. He is currently a Professor with the College of Automation, Harbin Engineering University. His current research interests include underwater navigation, integrated navigation technology and new inertial devices, high-precision navigation systems, and MEMS inertial navigation systems. MENGHAO LI received the B.S. degree from the College of Automation, Harbin Engineering University, Harbin, China, in 2016, where he is currently pursuing the Ph.D. degree in control science and engineering. His current research interests include MEMS inertial navigation systems, MEMS biaxial rotation modulation strapdown inertial navigation systems, information fusion, and its application in MEMS integrated navigation systems.