A method for analyzing the primary mirror deformation of photo-electronic theodolite with Zernike annular polynomials is researched. Firstly, a formula used to convert the finite element method (FEM) analysis results into the data based on the wave-front coordinate is deduced. Then, the deformation of the primary mirror in a photo-electronic theodolite is fitted with Zernike annular polynomials, and the peak-to-valley (PV) value (30.7 nm) and root-mean-square (RMS) value (6.3 nm) of surface error are calculated. Their error are 9.2% and 10.5% compared with actual inspection results. The influence of the primary mirror deformation on the aberration of optical system is obtained based on the relationship between Zernike annular polynomial coefficients and Seidel polynomial coefficients. Importing the Zernike annular polynomials into the Zemax software, a comprehensive analysis of the optical system can be realized. It provides information for optimizing the optical system.