In the exploration of the relationship between nutrition and health, dietary polyphenols, as bioactive substances derived from natural plants, have attracted much attention due to their diverse functional properties. Their health effects are highly dependent on the metabolic transformation by intestinal flora. The complex interaction between polyphenols and gut microbiota, as well as their role in the prevention and treatment of intestinal diseases, has become a research hotspot in the fields of nutrition and medicine. This review systematically explains the sources and classifications of polyphenols, points out their natural characteristic of low bioavailability. It also explores their intervention effects on intestinal diseases, analyzes the bidirectional action mechanism between polyphenols and gut microbiota, and elaborates on the specific pathways through which polyphenols improve intestinal diseases by regulating gut microbiota. Collectively, this review provides critical theoretical basis on polyphenols improving intestinal diseases for future research and clinical applications.