Anterior subapical segmental osteotomy is considered to be an important surgical technique to obtain functional occlusion and improve the facial profile for patients with maxillary and mandibular protrusion or retrusion, and some complications, such as ischemic necrosis of the distal segment, devitalization of the teeth adjacent to the osteotomy site, and inadequate movement space of segment for obtaining a good occlusion or facial profile, usually exist during surgery. Imprecise measurement of root length, interradicular distance, and intertooth distance based on traditional panoramic radiography that demonstrated existing horizontal distortion and vertical distortion may play an important role in resulting in these problems. In addition, the root is invisible for surgical simulation in traditional plaster models. The recently developed cone-beam computed tomography (CBCT) presents a higher spatial resolution with a lower radiation dose, simultaneously with excellent accuracy and without magnification of images. The presented technique was used to obtain a precise occlusal splint in virtual 3D subapical segmental osteotomy by combining CBCT with plaster models that could guarantee the measurement accuracy of root length, interradicular distance, and intertooth distance, followed by the result of fewer tooth root damage and more precise forecasting of available movement space of jaw segment. Combining with other advantages of virtual 3D surgery, such as precise teeth surface of plaster models, soft tissue simulation, genoplasty simulation, and zygoma plasty simulation, this presented technique may offer a preferable method to patients who need subapical segmental osteotomy.