[Objectives] The establishment of three-dimensional (3D) visual model of the skull of Saiga Antelope (Saiga tatarica) could be helpful in studying its anatomical features and further enhancing the accuracy of disease diagnosis as well as the effectiveness of species protection through “digital specimen”. [Methods] This study took the S. tatarica which is identified as an endangered species by State Forest Administration Gansu Protection Centre of Threatened Species as the research object. Cone-beam CT scanning and 3D reconstruction techniques were utilized to scan and reconstruct the skull of S. tatarica for morphological study. A total of 26 morphological parameters of the skull model were measured digitally with the measuring tool of the Mimics20.0 (Fig. 2), where the data were presented in the form of Mean ± SD. These results were compared with physical measurements obtained by vernier caliper and t-test between them was performed (Fig. 3). [Results] The high-precision 3D digital model of the skull of S. tatarica was successfully reconstructed. The reconstructed digital skull model could realize scaling and rotation, multi-angle cutting and measurement, and could better reflect the external characteristics, internal and three-dimensional structure of the head structure. The results showed that all the indexes (n = 8) had no significant difference from those obtained by physical measurements (P > 0.05). For example, for the full lengths of the skull obtained by vernier caliper and the digital model were 227.147 ± 10.646 mm and 227.130 ± 10.638 mm, respectively, similar between the “digital skull” and the dry skull (Table 1, P = 0.635). [Conclusion] This study has obtained the digital 3D model of the skull of S. tatarica, and compared the morphological characteristics of the skull using CT scanning and 3D reconstruction technology, which can provide the help for the diagnosis and treatment of head diseases as well as protection of this species. At the same time, it provides a theoretical basis for the clinical application and related research of CT scanning and 3D reconstruction in wild animals.