The aim of this study was to find an alternative method to meet traditional human anatomy teaching and clinical needs in order to solve the problem of cranial specimen attrition and specimen resource shortage due to long-term use. We performed a computed tomography (CT) scan of a well-preserved male cranial specimen and used Mimics 19.0 software for 3D reconstruction and cranial block separation. Subsequently, we compared the recognition ability of the processed cranial digital model with that of the 3D body digital model and used 3D printing to create the cranial model and compare it with the physical specimen. Twenty-two cranial bone block models were obtained, excluding the hyoid bone. Their 3D reconstructed digital models had better bony landmark recognition than the 3D body human digital models, and the differences between the 3D printed models and the physical specimens were minimal. In addition, only one stereolithography (STL) file was required to produce the cranial models, which facilitates repetitive printing at any time. By isolating cranial bone blocks through 3D reconstruction techniques and preparing high-quality cranial models in combination with 3D printing techniques, this study solves the problem of shortage of cranial teaching specimens for the sustainable development of clinical and medical schools.