The initial alignment of the polar region has the problem of collinearity between the gravity vector and the angular velocity of the earth rotation, increasing the difficulty of initial alignment in polar region. The analysis of navigation performance of initial error for the inertial navigation system (INS) is necessary to judge the initial alignment effect. In this paper, based on the algorithm of the transverse coordinate system of INS, the system error equation of the transverse mechanism is proposed to implement the analysis of navigation performance of initial error. Finally, the correctness of the error analysis and the applicability of transverse coordinate method are verified by simulation.