Because the accuracy of the existing airborne navigation is lacking in the polar region, it is difficult to ensure the safety and reliability of the aircraft when it is flying over the polar region. The integrated navigation system based on the inertial navigation technology uses multi-information fusion to assist collaborative navigation and obtain an indirect grid navigation algorithm that combines the azimuth navigation algorithm and the grid navigation algorithm to solve the existing problems. This paper analyzes the principle of the inertial navigation system in the polar region, the semiphysical simulation experiments are carried out by using the navigation theory and the background engineering, and the accuracies of the integrated navigation system of the indirect grid frame in the polar region and the integrated navigation system in the middle and low latitudes are consistent, which verifies the feasibility and effectiveness of the SINS/CNS/GPS integrated navigation system in the polar region. In addition, the paper provides the theoretical basis and the application of engineering to achieve the SINS/CNS/GPS integrated navigation system in the polar region.