The intestine is an important organ for digestion, absorption, and an immune barrier in the body, and maintaining its normal physiological function is crucial for the body health. Trace elements can regulate the expression of intestinal cell transporters, mucosal tight junction proteins, immune proteins, and Wnt signaling pathway-related proteins in intestinal stem cells, and play an important role in maintaining the integrity of the intestinal barrier, enhancing intestinal immune function, and promoting the proliferation and differentiation of intestinal stem cells. However, improper intake of trace elements may lead to intestinal damage and affect negatively intestinal functions. Therefore, it is of great significance to clarify the mechanisms underlying the regulatory effects of trace elements on intestinal function, to guide the rational dietary intake of trace elements. In this paper, the effects of trace elements such as iron, copper, and zinc on intestinal function are reviewed. The mechanisms of the regulatory actions of trace elements towards the intestinal barrier, digestion and absorption, and intestinal stem cells are described in detail. The negative impacts of insufficient or excessive trace elements on intestinal functions are also discussed, aiming to provide a theoretical basis for intestinal health-related research, and offer a theoretical basis and scientific guidance for rational intake of trace elements and the treatment of related diseases.