An automatic method of searching and matching sub-aperture for Shack-Hartmann Wavefront Sensor (SHWFS) is introduced to enlarge the dynamic range of SHWFS while maintaining its designed accuracy. Firstly, the threshold of the image is estimated. By taking a spot of near the center of the thresholded image as the reference center, other spots are searched horizontally and vertically and combined to retrieve the whole sub-aperture distribution. Finally, the sub-aperture distributions of two images are matched by shifting horizontally and vertically. The proposed method is verified experimentally. The result shows that this method can realize the automatic searching and matching of the sub-aperture of SHWFS and enlarge the dynamic range of SHWFS.