Based on the fast Fourier transform (FFT) algorithm, the wave-front reconstruction algorithm of Shack-Hartmann sensor is described. The fast Fourier transform is used to diagonalize and decouple the wave-front reconstruction equations which is deduced from the least-squares criterion. The algorithm is accurate and stable. And the superiority of real-time be comes notable when the Shack|Hartmann sensor′s spatial resolution is getting higher.