Shack-Hartmann sensor is widely used in adaptive optics systems, and laser beam quality measurements. The traditional method separates measures and calculations, and the wavefront reconstruction algorithm is slow to implement on the host computer. In this paper, the embedded GPU is introduced to Shack-Hartmann sensors' wavefront phase reconstruction. A parallel calculation method is proposed to speed up the wavefront phase reconstruction process. The experiment result shows the algorithm speed improves 50× with the image size of 2592×2048 pixels.