Performing surgeries on the craniocervical junction presents a technical challenge for operating surgeons. Three-dimensional (3D) reconstruction and surgical simulation have improved the efficacy and success rate of surgeries. The aim of this study was to create a 3D, digitized visible model of the craniocervical junction region to help realize accurate simulation of craniocervical surgery on a graphic workstation. Transverse sectional anatomy data for the study were chosen from the first Chinese visible human. Manual axial segmentation of the skull base, cervical spine, cerebellum, vertebral artery, internal carotid artery, sigmoid sinus, internal jugular vein, brain stem, and spinal cord were carried out by using Photoshop software. The segmented structures were reconstructed in 3 dimensions with surface and volume rendering to accurately display 3D models spatially. In contrast to conventional 3D reconstruction techniques that are based on computed tomography and magnetic resonance imaging Digital Imaging and Communications in Medicine (DICOM) inputs and provide mostly osseous details, this technique can help to illustrate the surrounding soft tissue structure and provide a realistic surgical simulation. The reconstructed 3D model was successfully used in simulating complex procedures in the virtual environment, including the transoral approach, bone drillings, and clivus resection.