The failure of the traditional initial alignment algorithm for the strapdown inertial navigation system (SINS) in high latitude is a significant challenge due to the rapid convergence of polar longitude. This paper presents a novel vision aided initial alignment method for the SINS of autonomous underwater vehicles (AUV) in polar regions. In this paper, we redesign the initial alignment model by combining inertial navigation mechanization equations in a transverse coordinate system (TCS) and visual measurement information obtained from a camera fixed on the vehicle. The observability of the proposed method is analyzed under different swing models, while the extended Kalman filter is chosen as an information fusion algorithm. Simulation results show that: the proposed method can improve the accuracy of the initial alignment for SINS in polar regions, and the deviation angle has a similar estimation accuracy in the case of uniaxial, biaxial, and triaxial swing modes, which is consistent with the results of the observable analysis.