In recent years, the research on metagenomics and metabonomics of intestinal flora has progressed rapidly, but the interaction with intestinal immune cells remains unclear. Group 3 innate lymphoid cells (ILC3) are a population of innate immune cells enriched in the intestinal mucosa, which is an important defense against intestinal microbial infection. On the one side, intestinal flora and its metabolites can directly or indirectly affect the development, proliferation and function of ILC3, and ILC3 may transform into different phenotypes and play a double-edged-sword role according to different microbial signals; on the other side, ILC3 can maintain the balance of resident microbiota and regulate responses of other immune cells to intestinal commensal bacteria. This article reviews the interaction between ILC3 and intestinal flora.