Objective To investigate the clinical effect of modified Shaoyao Decoction and Yunnan Hongyao rectal on the active stage of ulcerative colitis (UC). Methods A total of 70 UC patients admitted to Fuzhou Hospital of Traditional Chinese Medicine from August 2019 to September 2021 were selected as the research objects, and they were divided into control group and study group by alternate grouping method, with 35 patients in each group. Control group was treated with conventional treatment, and research group was treated with modified Shaoyao Decoction and Yunnan Hongyao rectal dripping on the basis of control group. Both groups were treated for 4 weeks. The traditional Chinese medicine syndrome score, modified Mayo score, Baron endoscopy score, serum C-reactive protein, lactobacillus, bifidobacteria and the incidence of adverse reactions were compared between the two groups. Results After 4 weeks of treatment, traditional Chinese medicine syndrome score, modified Mayo score and Baron endoscopy score of the study group were lower than those in the control group,and the differences were statistically significant (P<0.05). After 4 weeks of treatment, the level of serum C-reactive protein in the study group was lower than that in the control group, while the counts of Lactobacillus and Bifidobacteria were higher than those in the control group, and the differences were statistically significant (P<0.05). There were no obvious adverse reactions in the two groups during treatment. Conclusion Modified Shaoyao Decoction combined with Yunnan Hongyao rectal infusion can reduce the modified Mayo score,Baron endoscopy score and inflammatory factor levels in patients with active UC, improve the intestinal flora of the patients, reduce the clinical symptoms of the patients, and have good safety.