Shack–Hartmann wavefront sensor splits the incident wavefront into many subsections and transfers the distorted wavefront detection into the centroid measurement. The accuracy of the centroid measurement determines the accuracy of the SHWS. In this paper, we have presented an automatic centroid measurement method based on the image processing technology for practical applications of the digital SHWS in surface profile measurement. The method can detect the centroid of each focal spot accurately and robustly by eliminating the influences of various noises. Based on this centroid detection method, we have developed a digital SHWS system which can automatically detect centroids of focal spots, reconstruct the wavefront, and measure the 3D profile of the surface. The experimental results demonstrate that the system has good accuracy, repeatability and compatibility to optical misalignment. The system is suitable for online applications of surface measurement.