Flavonoids are a kind of polyphenolic compounds with 2-phenyl flavone structure， which are widely found in fruits， vegetables and tea leaves， and have the functions of anti-oxidation， reducing blood lipids， regulating blood glucose and inhibiting inflammation. Numerous studies have corroborated that the metabolic absorption and physiological function of flavonoids in vivo are closely related to gut microbiota. In this paper， we elucidated the interaction between flavonoids and gut microbiota from the structure and function of gut microbiota， types and products of microorganisms involved in metabolism， types and activities of metabolic enzymes and other aspects， summarized the mechanism of flavonoids in preventing obesity， diabetes， irritable bowel syndrome， cardiovascular disease and Alzheimer's disease by regulating gut microbiota， so as to provide theoretical basis for the application of flavonoids in functional foods.