The intestinal dysbacteriosis is closely associated with the occurrence and progress of radiation-induced intestinal injury. However, the specific mechanism remains unclear. Symbiotic bacteria in the human body play a significant role in maintaining the homeostasis of the intestinal microenvironment while participating in various physiological and pathological processes such as metabolism, immunoregulation, inflammation, and tumorigenesis. Ionizing radiation can destroy the intestinal epithelial barrier, creating an oxidative stress microenvironment. Consequently, the composition and structure of microbiota change, leading to dysbacteriosis through downstream inflammatory factors. Dysbacteriosis can further exacerbate radiation-induced intestinal injury by weakening the resistance of the intestinal epithelial barrier, activating inflammatory signaling pathways, and upregulating radiation-induced apoptosis response. The probiotic supplementation and fecal bacteria transplantation can reduce radiation-induced intestinal injury by regulating the balance of intestinal microbiota. This study reviews the advances in research on the pathogenesis and clinical protection of radiation enteritis based on gut microbiota, in order to provide a theoretical basis and reference for the prevention and treatment of radiation enteritis.