OBJECTIVE To investigate the small intestinal bacterial overgrowth (SIBO) and to evaluate the intestinal barrier function in ulcerative colitis (UC) patients treated with mesalazine and rifaximin. METHODS 96 patients undergoing the methane-hydrogen breath test in our hospital from January 2018 to January 2020 were enrolled in the study group, and 40 healthy persons were enrolled in the control group during this period. The SIBO positive rate of the two groups were collected and compared. Then, the SIBO positive patients were divided into group A and group B. Group A and group B all received mesalazine, and group B received rifaximin plus. The clinical efficacy, erythrocyte sedimentation rate (ESR), C reactive protein (CRP), and intestinal barrier function indexes like diamine oxidase (DAO) and D-lactic acid (DLA) were recorded and compared. RESULTS The study group presented higher SIBO positive rate compared with the control group (56% vs. 25%, P<0.05). After treatment, group B showed better clinical efficacy and lower levels of ESR and CRP than group A (all P<0.05). After treatment, the DAO and D-LA levels of the two groups were decreased, and presented lower levels in group B than group A (all P<0.05). CONCLUSIONS UC patients present a higher positive rate in SIBO. Mesalazine and rifaximin are applied to patients with mild to moderate UC, and their clinical efficacy has been significantly enhanced after the eradication of SIBO.