In aerial remote sensing field, auto-focus is one of the key problems to get high-quality images and applied to the certain fields, but real-time performance is poor. To improve calculating speed, the pixel-by-pixel overlapped sections in the three of frame images are selected as the gist for auto-focus algorithm. The auto-focus system consists of charge coupled device (CCD) camera, focusing mechanism, hardware circuit and so on. The new auto-focus algorithm combines captured overlapped areas and estimated similar frame difference method to search overlapped sections. In the overlapped sections, selecting the focusing evaluation function and step length realizes the transition from fast rough adjustment to accurate one and reaches the best state. The design of the software flowchart is given by using the focus value. The real flying experiment demonstrates that the auto-focus system improves the quality of image and the time of respond speed and minishes the burden of image processing software.