To analyze the effects of acupuncture and moxibustion on the relative abundance and diversity of gut microbiota in rats with Crohn's disease (CD) by 16S rDNA high-throughput sequencing and explore the mechanism of acupuncture and moxibustion on CD.Methods:Forty SD rats were randomly divided into a normal group，a model group，an indirect moxibustion group，an electroacupuncture (EA) group，and a western medicine group，with eight rats in each group.The CD model was induced in rats by enema with 2,4,6-trinitrobenzene sulfonic acid for four weeks.The bilateral “Tianshu” (ST 25) and “Qihai” (CV 6) were selected for intervention in the indirect moxibustion group and the EA group，and the rats in the western medicine group received sulfasalazine solution by gavage.After the intervention，the colon tissues and rat feces were collected for HE staining and 16S rDNA high-throughput sequencing，respectively.The sequencing results were analyzed for species relative abundance，alpha diversity，and functional gene prediction.Results:The histopathological scores of colon tissues of rats in the indirect moxibustion group and the EA group were significantly lower than those in the model group (P<0.01).Compared with the normal group，the model group showed the increased relative abundance of Bacteroidetes，Actinobacteria，Bacteroidia，Bacteroidales，Porphyromonadaceae，Prevotellaceae，Bacteroidaceae，and Prevotella，and the decreased relative abundance of Firmicutes，Proteobacteria，Clostrida，Clostridiales，Lachnospiraceae，Ruminococcaceae，and Lactobacillus.After indirect moxibustion and EA treatment，the relative abundance of the majority of the above-mentioned microorganisms improved to varying degrees.Compared with the normal group，the model group displayed decreased alpha diversity indexes of the gut microbiota，such as Chao1，Observed species，Shannon，and Simpson (P<0.05).Those indexes were elevated in the indirect moxibustion group and the EA group（P<0.05）as compared with those in the model group.As revealed by functional prediction analysis，both indirect moxibustion and EA could regulate functional genes involved in carbohydrate metabolism and amino acid metabolism.Conclusion:CD is related to changes in the structure of gut microbiota，and acupuncture and moxibustion can regulate the relative abundance and diversity of gut microbiota in CD rats.