Large errors of low-cost MEMS inertial measurement unit (MIMU) lead to huge navigation errors, even wrong navigation information. An integrated navigation system for unmanned vessel is proposed. It consists of a low-cost MIMU and Doppler velocity sonar (DVS). This paper presents an integrated navigation method, to improve the performance of navigation system. The integrated navigation system is tested using simulation and semi-physical simulation experiments, whose results show that attitude, velocity and position accuracy has improved awfully, giving exactly accurate navigation results. By means of the combination of low-cost MIMU and DVS, the proposed system is able to overcome fast drift problems of the low cost IMU.