Objective： To observe the clinical effect of warming-needle moxibustion combined with herbal cake-separated moxibustion on irritable bowel syndrome with diarrhea (IBS-D) and its effect on intestinal flora. Methods： A total of 100 cases of IBS-D patients were selected as study subjects and randomly divided into the observation group and the control group by using the envelope method，with 50 cases in each group. The control group was given Bifidobacterium Quadruple Viable Tablets orally on the basis of diet structure and lifestyle adjustment，and the observation group was additionally given warming-needle moxibustion and herbal cake-separated moxibustion on the basis of the control group. The levels of gastrointestinal hormones [(gastrin (GAS)， motilin (MTL)， and vasoactive intestinal peptide (VIP)]， the number of intestinal flora， and traditional Chinese medicine (TCM) syndrome scores before and after treatment，as well as clinical effects，were compared between the two groups. Results：After treatment， the total effective rate was 94.00% in the observation group and 76.00% in the control group， the difference being significant (P＜0.05). After treatment，the levels of GAS and MTL in the two groups were increased when compared with those before treatment (P＜0.05)， and VIP levels were decreased when compared with those before treatment (P＜0.05)；the levels of GAS and MTL in the observation group were higher than those in the control group (P＜0.05)，and the VIP level in the observation group was lower than that in the control group (P＜0.05). After treatment，the number of Lactobacilli and Bifidobacteria in the two groups was increased when compared with that before treatment (P＜0.05)， and the number of enterococci was decreased when compared with that before treatment (P＜0.05)； the number of Lactobacilli and Bifidobacteria in the observation group was higher than that in the control group (P＜0.05)， and the number of Enterococci in the observation group was lower than that in the control group (P＜0.05). After treatment， the scores of TCM syndromes including sloppy diarrhea, abdominal pain, mental fatigue, poor appetite and digestion, and bowel movement and flatus in the two groups were decreased when compared with those before treatment (P＜0.05)， and the above scores in the observation group were lower than those in the control group (P＜0.05). Conclusion：In the treatment of IBS-D，warming-needle moxibustion combined with herbal cake-separated moxibustion can effectively improve levels of gastrointestinal hormones and TCM syndromes of patients and adjust the number of intestinal flora with significant clinical effects.