ObjectiveTo investigate the possible mechanism of modified Gegen Qinlian Decoction （葛根芩连汤） in treatment of ulcerative colitis （UC） from the view of intestinal mucosal epithelial barrier damage and epithelial mesenchymal transition. MethodsSixty male C57BL/6J mice were divided into blank group， model group， western medicine control group， and low-， medium-， and high-dose modified Gegen Qinlian Decoction groups， with 10 mice in each group. Except for the blank group， 3% dextran sodium sulfate （DSS） was used to induce colitis model by free drinking for 7 days， and on the first day of modelling， 6， 12， and 24 g/（kg·d） of modified Gegen Qinlian Decoction were given to the low-， medium-， and high-dose groups respectively， 5-aminosalicylic acid （5-ASA） 100 mg/（kg·d） given by gavage to western medicine control group， and 10 ml/kg distilled water were given to blank and model group by gavage， once a day for 7 days. Body mass of mice was recorded and disease activity index （DAI） scores were performed daily. The mice were anesthetized after 24h of the last administration and the colon was taken to observe the length of colon， HE staining was applied to observe the damage of colonic mucosa and score pathological states， Masson staining to detect the deposition of colonic collagen fibers， immunofluorescence to observe the distribution of F-actin in colonic mucosal epithelium， and immunohistochemistry to detect the expression of tight junction protein ZO-1， Occludin， E-cadherin and Vimentin. ResultsCompared with the blank group at the same time， the percentage of body mass of mice in the model group on day 7 of modelling significantly reduced and the DAI score was significantly increased （P＜0.01）； compared with the model group at the same time， the body mass of mice in the western medicine control group and all of modified Gegen Qinlian Decoction groups decreased， and the DAI scores of mice in the western medicine control group and the high-dose modified Gegen Qinlian Decoction group decreased （P＜0.05 or P＜0.01）； compared with the same time of mice in the low-dos Gegen Qinlian Decoction group， the body mass of mice in the high-dose Gegen Qinlian Decoction group and the western medicine control group significantly elevated （P＜0.05）. Compared with the blank group， the length of the colon of mice in the model group was significantly shortened， the pathological score and the percentage of collagen area were significantly increased， the average fluorescence intensity of F-actin was reduced， the protein levels of ZO-1， Occludin and E-cadherin in the colon tissue decreased， and the protein level of Vimentin elevated （P＜0.01）. Compared with the model group， the length of colon significantly increased， patholo-gical score， collagen area percentage decreased， ZO-1， Occludin， E-cadherin protein levels increased and Vimentin levels decreased in all medicated groups； the average fluorescence intensity of F-actin increased in the western medicine control group and the middle- and high-dose Gegen Qinlian Decoction groups （P＜0.05 or P＜0.01）. Compared with the low-dose Gegen Qinlian Decoction group， the proportion of collagen fibre area in the middle-dose Gegen Qinlian Decoction group and the western medicine control group reduced； the mean fluorescence intensity of F-actin increased in the middle-dose Gegen Qinlian Decoction group； the protein levels of ZO-1 and E-cadherin increased in the western medicine control group， and the protein levels of ZO-1 increased in the high-dose Gegen Qinlian Decoction group （P＜0.05）. Compared with the medium-dose Gegen Qinlian Decoction group， the protein levels of ZO-1 elevated in the high-dose Gegen Qinlian Decoction group （P＜0.05）. Comapred with the high-dose Gegen Qinlian Decoction group， level of E-cadherin and Vimentin protein of the western medicine control group increased （P＜0.05）. ConclusionModified Gegen Qinlian Decoction was able to reduce colonic inflammation and mucosal barrier damage and inhibit the process of epithelial mesenchymal transition in mice models of ulcerative colitis， which may be one of its action mechanisms .