Objective To establish a rat model of superior mesenteric vein thrombosis by vein ligation and to simulate the pathological process of the disease, and to provide the basis for studies of its pathogenesis and treatment. Methods Ninety-six SPF male SD rats were randomly divided into three groups:Group A (sham operation group), group B (strangulation group) and group C (simple group), 32 rats in each group. Rats in group A were only opened the abdominal cavity but not blocked the blood supply. The rats were sacrificed at 8, 24, 48 and 72 h after operation. The rats in groups B and C were subjected to establish the strangulation and simple models by superior mesenteric vein thrombosis, respectively, and were sacrificed at 8, 24, 48 and 72 h after modeling. Histological changes (H&E staining) in the rat intestinal tissues were evaluated by a pathological scoring system. The levels of intestinal fatty acid binding protein (IFABP) and α-glutathione S-transferase (α-GST) were detected by ELISA. Results The rat model of mesenteric vein thrombosis was successfully established, with a success rate of 100% (96/96). The pathological analysis revealed that compared with the group A, different degrees of blood stasis and injuries were observed in the intestinal tissues of groups B and C, and the injury were gradually increased in the group B, while gradually reduced in the group C. The degrees of blood stasis and injury were positively correlated with the scope of ligation. The result of ELISA showed that the serum levels of IFABP and α-GST of the rats in groups B and C were significantly higher than those in group A (P < 0.05), and the degree of elevation was positively correlated with the scope of ligation. Conclusions In this study, the rat model of superior mesenteric vein thrombosis is successfully established by vein ligation. This model is simple and easy to operate with a high success rate, and can be used in related research.