MGN-3 is an arabinoxylan from rice bran that has been shown to be an excellent antioxidant and radioprotector. This study examined the protective effects of MGN-3 on radiation-induced intestinal injury. Mice were treated with MGN-3 prior to irradiation, then continued to receive MGN-3 for 4 weeks thereafter. MGN-3 increased the activity of mitochondrial respiratory chain complexes Ⅰ, Ⅲ, Ⅳ and Ⅴ, the intercellular ATP content, the mitochondria-encoded gene expression and mitochondrial copy numbers in the jejunal and colonic mucosa. MGN-3 reduced the oxidative stress levels and inflammatory response indicators in the serum and jejunal and colonic mucosa. Antioxidant indicators such as superoxide dismutase, glutathione peroxidase, catalase and total antioxidant capacity were significantly increased in the serum and jejunal and colonic mucosa in the MGN-3 group. Moreover, MGN-3 decreased the gene abundances and enzymatic activities of caspase-3, 8, 9 and 10 in the jejunal and colonic mucosa. The endotoxin, diamine peroxidase, d-lactate and zonulin levels were significantly reduced in the serum and jejunal and colonic mucosa in the MGN-3 group. MGN-3 also markedly upregulated the gene abundances of ZO-1, occludin, claudin-1 and mucin 2. MGN-3 effectively attenuated radiation-induced changes in the intestinal epithelial mitochondrial function, oxidative stress, inflammatory response, apoptosis, intestinal permeability and barrier function in mice. These findings add to our understanding of the potential mechanisms by which MGN-3 alleviates radioactive intestinal injury.