The gravity tends to coincide with the earth’s rotation vector in the polar region, degrading the coarse alignment azimuth of the strapdown inertial navigation system (SINS) to a large misalignment. Under a large azimuth misalignment, the linear error model inevitably renders unacceptable theoretical errors in the integrated alignment. In addition, polar region challenge such sensors as a star sensor of celestial navigation, which fails to provide high-precision attitude reference for integrated alignment. Therefore, in allusion to the misalignment mentioned above based on SINS for the polar region, an integrated alignment algorithm is proposed, assisted by the Doppler Velocity Log (DVL). Notably, the work first investigates the extent to which azimuth accuracy deteriorates in the polar region. On the premise of large azimuth misalignment, the nonlinear error model under the transverse frame is derived from the ellipsoid earth model. Additionally, the state and measurement models are constructed, combined with the velocity of DVL as an observation. An adaptive measurement variance matrix is designed for the unscented Kalman filter (UKF) to estimate the attitude error. Eventually, the semi-physical experiments demonstrate that the proposed algorithm significantly improves the initial alignment accuracy of the polar region.