Abstract To improve the alignment accuracy and environmental applicability of the micro-electromechanical system (MEMS)-based strapdown inertial navigation system (SINS), this study proposes a global navigation satellite system (GNSS)-assisted multi-vector determination of the attitude optimal indirect coarse alignment. Using the inertial information output from the inertial measurement unit and the velocity information from the GNSS, a simplified velocity observation vector is constructed and the velocity lever arm stemming from the mounting position inconsistencies of the GNSS and SINS is fed back into the velocity of the carrier system. When constructing the observation vectors, the integration interval is shortened by reconstructing the two-vector integration formula for reducing the cumulative error of the inertial device. The attitude matrix problem is defined as the Wahba problem, which is solved using the singular value decomposition method. Based on the relationship between gyro zero bias and misalignment angle, the corresponding state and measurement equations are designed. Furthermore, owing to the measurement noise uncertainty, the adaptive traceless Kalman filtering algorithm is introduced to realize the effective adaptation processing of the measurement noise. More accurate attitude matrix estimates are obtained by continuously correcting the carrier system transformation matrix. The running car experiment results show that the proposed method exhibits higher alignment accuracy and environmental applicability than the current MEMS strapdown inertial navigation coarse alignment method and the traditional optimization-based alignment method.