To explore the effects of Chaiqi Decoction on gut microbiota in metabolic syndrome rats based on high-throughput 16S rRNA gene sequencing.Methods:Illumina Miseq PE300 high-throughput sequencer was used to detect the 16S rRNA gene V3-V4 variable region of rat fecal intestinal flora.Usearch，Mothur，and LEfSe were used to analyze the composition and structure of intestinal flora and the relative abundance of different bacteria.Results:Chaiqi Decoction can reverse the decline in the species diversity of the intestinal flora of rats with metabolic syndrome and correct the changes in the composition and structure of the flora caused by the metabolic syndrome.The study found that the relative abundance of 57 genera of the intestinal flora of rats with metabolic syndrome changed significantly at the level of genus，and Chaiqi Decoction could restore 54 of them to normal levels.Conclusion:The possible pathogenesis of metabolic syndrome from the perspective of intestinal microecology is explained.Chaiqi Decoction could prevent and treat metabolic syndrome by regulating the intestinal flora.