Objective The purpose of the present study was to investigate the influence of intermittent hypoxia on gut microbiota in OSAS rat models.Methods 6 rats were randomly divided into the normoxic group (NC group) and the intermittent hypoxia group (IH group), with 8 rats in each group. At the end of the 4-week intermittent hypoxia or normoxic treatment experiment, feces of each rat were collected to extract DNA. Microbiome composition was determined by 16S rRNA pyrosequencing and bioinformatic analysis. Welch T test and ANOSIM was used to analyze α diversity and β diversity between the two groups, respectively. KW sum-rank test was conducted to analyze abundance difference between the two groups.Results There is no significant difference in the number of OTUs between IH group and NC group (P＞0.05). And no significant differences in community diversity (Shannon index) and community richness (Chao1 index) between the two groups were found(P＞0.05). Then the structure of the gut microbiome was examined by Lefse software and the LDA score was used to estimate the effect of abundance of each species on the difference between IH group and NC group. The results showed that, at the level of phylum, Bacteroidetes (P＜0.05) and Tenericutes (P＜0.001) were significantly enriched in IH group, while Firmicutes (P＜0.05) were significantly enriched in NC group. However, We found no significant difference between IH and NC groups in terms of the abundance of Proteobacterias (P＞0.05).At the family level, among the 12 dominant bacteria, Prevotellaceae (P＜0.05), Christensenellaceae (P＜ 0.001), Erysipelotrichaceae(P＜0.05), Mollicutes_RF9 (P＜0.01) were significantly enriched in IH group, while Rikenellaceae (P＜0.001) and Lactobacillaceae (P＜0.01)were significantly enriched in NC group. In the disadvantaged bacteria, Alcaligenaceae (P＜0.01), Rhodospirillaceae (P＜0.05), vadinBE97(P＜0.05) showed significant enrichment in IH group. Network analyses and single factor correlation network analysis revealed extensive interactions among the identified species between the IH and NC groups.Conclusion Although intermittent hypoxia did not change the community diversity and richness, it has a significant influence on the structure of the gut microbiome in OSAS rat model.