Regarding the influence to the inertial navigation system of missile by disturbing gravity was focused, a polynomial fitting method was used to express disturbing gravity along the trajectory, and an analytical expression for calculating the deviation from the nominal value without considering disturbing gravity was deduced based on the linear system theory and the perturbation theory. Moreover, the coupling property between disturbing gravity and apparent acceleration was considered. The apparent acceleration deviation caused by disturbing gravity was regarded as an additional term of disturbing gravity, and was corrected by iterative method. The simulation results show that the error of disturbing gravity fitting method is less than 3×10^-7m/s², and the residual error of the analytical formula considering the compensation of the apparent acceleration deviation is about 1/3 of the original method, and the computation time is only 1/10 of the numerical integration method.