This study investigates the therapeutic effects of Qingchang Yuyang Decoction on ulcerative colitis (UC) and its impact on intestinal flora. Using existing case records, a retrospective analysis was conducted utilizing clinical data from 96 UC patients (damp-heat syndrome of the large intestine) treated at our hospital between June 2022 and June 2024. Based on the different treatment methods recorded, 50 patients were included in the observation group and 46 in the control group. The control group received conventional treatment (oral sustained-release mesalazine tablets), while the observation group received oral Qingchang Yuyang Decoction in addition to conventional treatment. The efficacy and effects on intestinal flora were compared between the two groups. The change in the modified Mayo score before and after treatment in the observation group was significantly greater than that in the control group (p < 0.001). After treatment, scores for abdominal pain and diarrhea, mucus-pus-bloody stools, tenesmus, anal burning, and short and red urine were significantly lower in the observation group compared to the control group (p < 0.05). Post-treatment, the observation group showed significantly higher levels of IL-10 than the control group, while IL-8 and TNF-alpha levels were lower in the observation group (p < 0.05). After treatment, Enterococcus and Enterobacter counts in the observation group were lower, while the observation group had higher levels of Bifidobacterium, Butyric Clostridium, and Lactobacillus compared to the control group (p < 0.05). The complication rate was lower in the observation group (p < 0.05). The combination of Qingchang Yuyang Decoction with sustained-release mesalazine tablets can improve the clinical efficacy in UC, significantly alleviate clinical symptoms, reduce the inflammatory response, adjust intestinal flora distribution, and promote recovery, making it worthy of clinical application.