Abstract: Inflammatory bowel disease(IBD) is a chronic inflammatory disease of the intestine, mainly manifested by the infiltration of inflammatory cells in the intestine and damage of the intestinal mucosa. This incidence is gradually increasing in Asian countries. Conventional treatments for IBD include antibiotics and immunosuppressants, which are highly toxic, could induce super pathogens, and even cause some damage to the immune system. Flavonoids, a class of natural substances with variable phenol structure, have anti-oxidation and anti-inflammatory properties. Moreover, natural products of flavonoids are widely found in nature and have been proven to prevent and treat intestinal inflammation, but the specific mechanism of action remains unclear. This review discussed the interrelationship between intestinal microbiota and the pathogenesis of inflammatory bowel disease, and how flavonoids reduced the general intestinal microbiota imbalance and the increase of pro-inflammatory factors in IBD patients by regulating intestinal microbiota so as to relieve symptoms. It was aimed to explore the mechanism of flavonoids in improving inflammatory bowel disease by studying the bacteriostatic and immunomodulatory effects of natural flavonoids. This review will provide some theoretical guidance for the application of flavonoids in the improvement of inflammatory bowel disease and the exploration of its mechanism.