In this article, the in-motion polar alignment method for strapdown inertial navigation system (SINS)/global positioning system (GPS) integration is proposed. First, to address the defects of the fast convergence of the longitude with the navigational mechanization, the unified navigation mechanization is used to construct the vector observations for the in-motion alignment method. Second, the initial velocity errors, which are generated by the GPS outputs, are considered. To suppress the initial velocity errors, the improved vector observation with the vector subtraction improvements is investigated. With the vector subtraction improvements, the initial velocity errors are eliminated efficiently. Third, to enhance the correction of the observation vectors for the attitude determination, the continuous attitude determination method with the expansion samples of the GPS outputs is designed. Lastly, to verify the performance of the proposed method, the virtual polar region technology in the transverse mechanization is devised. The simulation and field tests are designed for verification, the test results are shown that the proposed method can finish the in-motion polar alignment process, and the initial velocity errors are suppressed. Moreover, the subtraction operation for observation vectors does not degrade the performance of the alignment process.