In order to improve the accuracy of dynamic 3-D shape measurement by fringe projection, the windowed Fourier analysis was used to reduce the phase shift error caused by motion. Firstly, the actual phase shift between deformed fringes was estimated by windowed Fourier analysis. Then, the phase distribution of the deformed fringes was estimated with high precision by the least square method. Finally, 3-D shape of the scene was obtained from the estimated phase calculation. The influence of object motion on phase shift was analyzed theoretically. The phase shift estimation accuracy of the proposed method was studied by simulation. An experimental system was built to verify the results. The phase recovery accuracy of the proposed method is 0.1673rad. Compared with the existing methods, this method is obviously improved. The results show that the method is effective.