When traditional error correction methods are used in microsphere surface inspection, it might show a larger residual. Therefore, this paper proposes a surface topography to correct the eccentricity of microsphere and to improve the measuring precision and efficiency. Based on the analysis of mathematic model of optical path difference introduced by the lateral and axial eccentricities, the high-order approximation model of eccentricity error was deduced. A eccentricity correction method for small sphere curvature radius was proposed on the basis of Zernike polynomials fitting. The correction flow was provided for illustrating the detail, and the corresponding calibration method of relative parameters was given. An experiment for the surface topography of a microphere with a diameter of 2 mm was performed to verify the feasibility and effectiveness of the correction method. The experimental results relative to the standard profile data indicate that the proposed correction method offers the surface errors(peak-valley(PV) and root-mean-square(RMS) values) to be 0.081 5λ and 0.016 1λ, respectively, which are more excellent than that of the traditional methods. The method is able to meet the demand of high precise inspection of microspheres.