This paper is concerned with a three-dimensional (3D) analysis on soft and hard tissue changes after mandibular setback surgery. For comparing with previous two-dimensional (2D) cephalometric data, we proposed a three-dimensional registration and analysis method based on the cephalometric knowledge. The 3D changes of bone, soft tissue and the ratio of soft tissue to bony movement were investigated in eight skeletal class III mandibular prognathism patients. CT scans of each patient were taken at pre- and post-operative states. Each scan was registered to a universal 3D coordinate system defined by cephalometric landmarks. A grid, parallel to the coronal plane, was also designed for the comparison of the changes. The bone and soft tissue was intersected by the projected line from each point on the grid. The coordinate values of intersected point were measured and compared between the pre- and post-operative models. In addition, the reproducibility of the universal coordinate system and the grid was evaluated. The facial surface changes after setback surgery occurred not only in the mandible but also in the mouth corner region. The soft tissue changes of the mandible were measured relatively by the proportional ratios to the bone changes. The ratios at the mid-sagittal plane were 77-102% (p<0.05). The ratios at all other sagittal planes had similar patterns to the mid-sagittal plane with decreased values. All the results conformed to the previous 2D based clinical knowledge and instinct of orthodontists. It is expected that the proposed approach would be applicable to other oral and maxillofacial surgeries as well as plastic surgeries.