Objective To establish a visualization model of CT three-dimensional reconstruction of tree shrew skeletal system and to provide a basis for diagnosis of tree shrew skeletal system diseases. Methods We used Toshiba Aquillon One 320 row helical CT scan (voltage: 100 kV, electric current: 80 mA, bulb revolution: 0.35 s/roll, pitch: 1.35, image set: 0.5 mm, layer spacing: 0.5 mm, algorithm: bone reconstruction method, and we used volume imaging (VR), multi-planar imaging (MPR) and surface imaging technology by choosing Musculoskeletal CT option of Vitrea package in the parallel computing environment for 3D reconstruction. Results The reconstruction of visual model structure is distinct, clear, allowing to truly reappear the tree shrew skeletal system in the 3D computer model. In this model, we identified five ridges on the back of the skull, and located four big holes in the lateral view. In addition, we showed some smaller skull holes, such as optic foramen and submandibular foramen. We determined the quantitative data of the tree shrew skeleton system more precisely and comprehensively. We also found some abnormal data in tree shrews, such as pelvic asymmetry, increased thorax, bone fracture and calcification in the synovial bursa. Conclusions The established CT 3-D visualization technique can determine special features of the skeletal system in tree shrews non-invasively, which is very important for ecological classification, identification, and evolution analysis of tree shrews.