By analyzing the error models of the measured vectors of the gravitational apparent motion, an in-motion filter-QUEST alignment method only with the inertial measurement unit is presented in this paper. The contribution of the proposed method lies in constructing the in-motion model of the measured vectors of the gravitational apparent motion and developing the extracted method to reconstruct the measured vectors. Furthermore, the relationship between the noise characteristic and the moving state of the vehicle is analyzed in detail. Different from the several current techniques, the presented method can be carried out without any other external additional equipment, when the vehicle is in-motion. With the designed real-time wavelet denoising (RWD) method, the high-frequency noises of the measured vectors are filtered. Based on the constructed parameter recognition model of the measured vectors, a robust adaptive Kalman filter is devised to estimate the optimal parameters, which are used to calculate the reconstructed observation vectors. Moreover, the gross outliers, which are contained in the filtered vectors of the RWD, are eliminated effectively. The simulation and the field trial results demonstrate that the presented method is applicable to the in-motion initial alignment, and it can serve as a nice initial alignment method in the follow-on fine alignment process and navigation process.