Objective Observe and analyse the clinical efficacy of compound Baitouweng decoction combined with Western medicine in the treatment of refractory amoebic enteritis complicated by ulcerative colitis, as well as changes in intestinal microbiota, providing reference for the clinical diagnosis and treatment of refractory amoebic enteritis complicated by ulcerative colitis. Methods Collect patients who meet the diagnostic criteria for ulcerative colitis complicated with refractory amoebic enteritis They were treated with compound Baitouweng decoction combined with Western medicine. Stool samples were collected before treatment, 4 weeks after treatment, and 8 weeks after treatment. The final samples were subjected to high-throughput sequencing and metabolomics testing, and correlation analysis was conducted based on the patient’s symptom score. Results 1. Clearance of amoebic trophoblasts and cysts: After 8 weeks of treatment, among the 12 enrolled patients, 11 patients did not show amoebic trophoblasts and cysts in their stool routine, and 1 patient showed amoebic cysts in his stool routine microscopy. The total effective rate was 91.7%. After extending the treatment for 10 days, no entamoeba histolytica trophozoites or cysts were found in the patient’s stool routine examination. At this time, the total effective rate reached 100%. 2. Changes in symptom scores: (1) Comparison of total scores: The scores of UC patients with refractory amoebic enteritis decreased significantly compared to before treatment, and the difference was statistically significant (P<0.05). (2) Comparison of scores for individual symptoms: The scores for both primary and secondary symptoms decreased significantly compared to before treatment, and the difference was statistically significant(P<0.05); 3. Changes in gut microbiota and metabolomics analysis before and after treatment: (1) After treatment, the abundance and diversity of gut microbiota in patients showed significant changes in both alpha and beta diversity, with statistical significance(P<0.05). (2) Species composition and differential analysis: ① At the phylum level, before treatment, the patient’s gut microbiota was mainly composed of Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes, which accounted for over 90% of the total. After treatment, Firmicutes, Proteobacteria, and Bacteroidetes dominated, while the proportion of Actinobacteria decreased At the genus level, compared with before treatment, the number of protective bacteria such as Bacteroides, Faecalibacterium, and Streptococcus in the patient’s stool significantly increased, while invasive bacteria such as Escherichia coli Shigella, Haemophilus, and Clostridium were significantly reduced. (3) Metabolomics and differential analysis: Metabolomics analysis of fecal samples from patients after treatment showed significant differences in metabolic pathways, glycerophospholipid metabolism pathways, and biosynthesis of secondary metabolites. Among them, substances with significant differences include indole-3-lactic acid, L-carnitine, phosphatidylcholine, etc., and the differences are statistically significant(P<0.05). Conclusion The use of compound Baitouweng decoction combined with Western medicine can effectively treat and kill intestinal Amoebic Trophoblasts and Cysts in the treatment of UC complicated refractory amoebic enteritis. It can effectively alleviate patients’ symptoms, improve clinical efficacy, and improve patients’ TCM syndrome scores. The mechanism may be related to improving the structure and metabolomics of intestinal microbiota, thereby improving the intestinal microbiota environment and metabolic pathways, and playing an auxiliary anti-inflammatory role. It can provide reference for the clinical treatment of UC complicated refractory amoebic enteritis.