Three-dimensional point cloud data can be obtained from fringe projection method. However, these point cloud data may have holes for complex shaped objects, and the holes have a profound impact on afterward processing. According to structure from motion (SFM) data acquisition, we propose a new method to repair holes. Firstly, we use a two-dimensional phase of fringe projection to extract boundary points from the three-dimensional point cloud. Then, we register the data set obtained from SFM and fringe projection to extract supplementary points. Finally, based on the point cloud data set with supplementary points, the repair of point cloud holes is implemented based on the radial basis function to calculate the surface equation. Experimental results show that the algorithm is robust and it can recover the surface information of complex objects effectively.