How to create an efficient and accurate interactive tool for triangular mesh clipping is one of the key problems to be solved in computer-assisted surgical planning. Although the existing algorithms can realize three-dimensional model clipping, problems still remain unsolved regarding the flexibility of clipping paths and the capping of clipped cross-sections. In this study, we propose a mesh clipping algorithm for surgical planning based on polygonal convex partitioning. First, two-dimensional polygonal regions are extended to three-dimensional clipping paths generated from selected reference points. Second, the convex regions are partitioned with a recursive algorithm to obtain the clipped and residual models with closed surfaces. Finally, surgical planning software with the function of mesh clipping has been developed, which is capable to create complex clipping paths by normal vector adjustment and thickness control. The robustness and efficiency of our algorithm have been demonstrated by surgical planning of craniomaxillofacial osteotomy, pelvis tumor resection and cranial vault remodeling.