Through-focus scanning optical microscopy (TSOM) is a high-efficient, low-costed, and nondestructive model-based optical nanoscale method with the capability of measuring semiconductor targets from nanometer to micrometer level. However, some instability issues resulted from lateral movement of the target and angular illuminating non-uniformity during the collection of through-focus (TF) images restrict TSOM's potential applications so that considerable efforts are needed to align optical elements before the collection and correct the experimental TSOM image before differentiating the experimental TSOM image from simulated TSOM image. An improved corrected TSOM method using Fourier transform is herein presented in this paper. First, a series of experimental TF images are collected through scanning the objective of the optical microscopy, and the ideally simulated TF images are obtained by a full-vector formulation. Then, each experimental image is aligned to its corresponding simulated counterpart before constructing the TSOM image. Based on the analysis of precision and repeatability, this method demonstrates its capability to improve the performance of TSOM, and the promising possibilities in application of online and in-machine measurements.