Radiation-induced intestinal injury is a common complication of abdominal radiation therapy. However, the pathological features of radiation-induced intestinal injury and its therapeutic regimen are not very clear. The aim of this study was to investigate the effects of antibiotic pretreatment on radiation-induced intestinal injury. Abdominal radiation disrupted the intestinal microbiota balance and significantly reduced bacterial diversity in mice. Antibiotic cocktail (Abx) pretreatment effectively removed the intestinal microbiota of mice, and metronidazole also reduced the diversity of intestinal bacteria to some extent. Two antibiotic pretreatment regimens improved the reconstitution ability of the gut microbiota in mice after radiation. Further experiments showed that Abx pretreatment effectively reduced the content of lipopolysaccharide (LPS) and inhibited the TLR4/MyD88/NF-κB signaling pathway in the ileum. In addition, Abx pretreatment regulated macrophage cell polarization in the ileum, downregulated TGF-β1, phosphorylated Smad-3 and α-SMA protein levels, and upregulated E-cadherin protein expression. Eventually, Abx pretreatment significantly improved the survival rate and attenuated intestinal injury of mice after radiation by reducing inflammation and preventing intestinal fibrosis. These results revealed that antibiotic pretreatment can effectively alleviate gut microbiota turbulence and intestinal damage caused by abdominal radiation in mice. Collectively, these findings add to our understanding of the pathogenesis of radiation enteritis.