Flavonoids are phytochemicals that widely exist in plants, fruits, and vegetables and have a variety of activities. However, due to their complex structure, it is often rarely absorbed into the blood. Intestinal bacteria regarded as the third kind of human organ have attracted extensive attention in recent years. Complex structural flavonoids can be catabolized into low molecular weight phenolic acids under the action of intestinal bacteria and then absorbed into the blood, showing several protective effects on the body. In addition, the intake of flavonoids can also regulate the composition and function of intestinal flora. This paper comprehensively summarizes the interaction between flavonoids and intestinal flora, as well as the impact on human health, in order to provide some insights on how to combine intestinal microorganisms to select and ingest dietary polyphenols for future applications in medicine.