In three-dimensional (3D) shape measurement based on fringe projection, various factors can degrade the quality of the point cloud. Existing point cloud filtering methods involve analyzing the geometric relationship between 3D space and point cloud, which poses challenges such as complex calculation and low efficiency. To improve the accuracy and speed of point cloud filtering, this paper proposes a new point cloud filtering method based on image segmentation and the absolute phase for the 3D imaging obtained by fringe projection. Firstly, a two-dimensional (2D) point cloud mapping image is established based on the 3D point cloud obtained from fringe projection. Secondly, threshold segmentation and region growing methods are used to segment the 2D point cloud mapping image, followed by recording and removal of the segmented noise region. Using the relationship between the noise point cloud and the absolute phase noise point in fringe projection, a reference noise-free point is established, and the absolute phase line segment is restored to obtain the absolute phase of the noise-free point. Finally, a new 2D point cloud mapping image is reconstructed in 3D space to obtain a point cloud with noise removed. Experimental results show that the point cloud denoising accuracy calculated by this method can reach up to 99.974%, and the running time is 0.954 s. The proposed method can effectively remove point cloud noise and avoid complex calculations in 3D space. This method can not only remove the noise of the 3D point cloud but also can restore the partly removed noise point cloud into a noise-free 3D point cloud, which can improve the accuracy of the 3D point cloud.