A wide variety and numerous microorganisms, collectively known as microbiota, reside in the intestine, which substantially promote the nutrient absorption, metabolism, and immune regulation of hosts. However, dysregulated or translocated gut microbiota contributes to the development of many diseases. As the primary barrier for the body to encounter intestinal microorganisms, the intestinal epithelial cells (IECs) play a crucial role in responding to intestinal microbial colonization, regulating intestinal microbial community structure, and maintaining intestinal mucosal barrier function. Here, we review the latest advances in our knowledge of how the interactions between the microbiota and IECs regulate the mucosal immune function in the gut.