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Abstract: Objective To study the rat brain trauma injury model and investigate the rules of transformation of expression of synaptophysin and its relationship between histology and radiology alternation after brain trauma injury. Methods 24 SD male rats aged three months were randomly divided into 4 groups, including a control group of 6 rats. The experimental group rats were received operation to build free falling brain trauma injury model. The rat were analyzed at 2, 4, 8 weeks after injury. The experimental group rat were killed after CT scan and functional evaluation, histological changes were measured through HE staining. Synaptophysin were observed by using immunofluorescence method and Western blot. Results After brain injury the functional evaluation of rat showed dysneuria. Edema and necrosis in neurons and local congestion at 24 h after injury, necrosis and solubility liquefaction at 2 weeks after injury, and histological defects at 4 weeks and 8 weeks after injury, were observed in HE staining in experimental group. The significant cerebral low density shadows at 24 h after injury, lightened in 2 weeks after injury, and disappeared at 4 weeks and 8 weeks after injury, left only the bone defects in CT images. Expression of synaptophysin in brain tissue was decreased from 2 weeks after injury and it was mild increased at 8 weeks after injury evaluated by immunofluorescence method and Western blot. Conclusion The functional evaluation, histological and CT scan result indicate that we have built the rat brain trauma injury model successfully. The damage of synapse was correlated with histological and radiological result. The expression of synaptophysin was decreased form acute stage and gradually increased until 8 weeks after injury. This study can be applied as control in research of nerve regeneration after brain trauma injury.