Objective To observe small intestinal bacterial overgrowth（SIBO）and oral cecal transit time （OCTT）in patients with ulcerative colitis，the therapeutic effect of rifaximin combined with Bacillus subtilis were investigated. Methods All of the people enrolled in the study（UC group = 100 cases，healthy group = 50 cases） were tested for SIBO and OCTT. UC patients with SIBO were randomly divided into two groups：control group： Bacillus subtilis（500 mg，3/d，14 d）；Treatment group：Bacillus subtilis（500 mg，3/d，14 d）and Rifaximin（0.2 g， 4/d，14 d）. After treatment，interleukin⁃6（IL⁃6）and C⁃reactive protein（CRP）were observed. Results （1）SIBO in patients with ulcerative colitis was 41.0%，and that in healthy control group was 18.0%（P < 0.05）. The inci⁃ dence of SIBO was not related to gender and age（P > 0.05）.（2）OCTT in patients with ulcerative colitis was （128.8 ± 20.3）min，and in that control group was（90.7 ± 13.6）min（P < 0.05）（. 3）The OCTT of ulcerative colitis patients with SIBO was（150.5 ± 22.6）min，and in that of patients without SIBO was（108.3 ± 19.7）min（P < 0.05）. （4）65% of the patients in the treatment group turned negative and 23.8% of the patients in the control group turned negative（P < 0.05）.（5）In the treatment group：IL ⁃ 6 and CRP were significantly lower：IL ⁃ 6（50.16 ± 8.5）vs. （20.31 ± 7.1）and CRP（33.36 ± 3.4）vs.（10.22 ± 4.1）（P < 0.05）. Conclusions Patients with ulcerative colitis had a high probability of SIBO. Rrifaximin combined with Bacillus subtilis can effectively alleviate inflammation.