Since the PMF’s polarization axis alignment method based on image processing of PMF’s end, has been researched and applied more and more, manual focus predominates in the image-processing alignment system. Consequently, an autofocus system is built, and an autofocus algorithm based on the imaging characteristic of alignment system is presented. The variance function is selected to evaluate image definition, with a focusing window selection method based on local variance maximum to enhance its sensitivity. Additionally, a comprehensive strategy based on iterative fitting is designed to search for image focus. The experiment results indicate that this algorithm can realize the focusing of PMF and its gasket both fast and stably.