Background: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium.Methods: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies.Results: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P < 0.01). Moxibustion treatment increased abundance levels ofBacteroidetes,Actinobacteria,Ascomycota,Synergistetesand decreased abundance ofFirmicutes,Proteobacteria. At the genus level, the abundance ofBacteroides,Bacteroides_bacterium_M7,Prevotella,Bacteroidales_bacterium_H2, were increased andBacteroides_bacterium_H3,Parabacteroides,Porphyromonas,Alistipes,Parasutterellawere decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance ofBacteroidesandBacteroides_bacterium_H3and decreasedBacteroides_bacterium_M7,Prevotella,Bacteroidales_bacterium_H2. In UC group, the specieBacteroides_massiliensiswas negatively (P < 0.05) correlated with IL-23,Bacteroides_eggerthii_CAG109andBacteroides_eggerthiiwere negatively (P < 0.05) correlated with TGF-β. And the speciesPrevotella_sp_CAG1031andBacteroides_bacterium_H2were significant positively (P < 0.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment.Conclusions: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.