Diet can be considered as one of the pivotal factors in regulating gastrointestinal health, and polyphenols widely distributed in human daily diet. The polyphenols and their metabolites playing a series of beneficial effects in human gastrointestinal tract that can regulate of the gut microbiota, increase intestinal barrier function, repair gastrointestinal mucosa, reduce oxidative stress, inhibit the secretion of inflammatory factors and regulating immune function, and their absorption and biotransformation mainly depend on the activity of intestinal microflora. However, little is known about the two-way interaction between polyphenols and intestinal microbiota. The objective of this review is to highlight the structure optimization and effect of flavonoids on intestinal flora, and discusses the mechanisms of dietary flavonoids regulating intestinal flora. The multiple effects of single molecule of flavonoids, and inter-dependence between the gut microbiota and polyphenol metabolites. Moreover, the protective effects of polyphenols on intestinal barrier function, and effects of interaction between plant polyphenols and macromolecules on gastrointestinal health. This review provided valuable insight that may be useful for better understanding the mechanism of the gastrointestinal health effects of polyphenols, and provide a scientific basis for their application as functional food.