Scope Gastrointestinal side effects are frequently observed in patients receiving medical radiation therapy. As Lacticaseibacillus casei ATCC334 potentially affects microbial ecosystem, the study hypothesizes that it may improve radiation‐induced intestinal injury in rats by modulating the “gut microbiota‐metabolite‐barrier axis.” Methods and results Rats are fed one of three or no doses of L. casei ATCC334 for 7 days and then expose to a single dose of 9 Gy X‐ray total abdominal irradiation. Supplementation with L. casei ATCC334 promote the proliferation of intestinal stem cells (ISCs), increase the expression of tight junction proteins, reduce intestinal permeability, and protect intestinal barrier integrity. Moreover, 16S rRNA sequencing show that medium and high doses of L. casei ATCC334 inhibit the growth of Escherichia/Shigella and favor Akkermansia proliferation. L. casei ATCC334 intervention reprogram the metabolic profile and inhibit putrescine production but promote alpha‐linolenic acid (ALA) production. Notably, a decrease in putrescine and an increase in ALA are significantly correlated with the proliferation of ISCs and enhanced intestinal barrier function following L. casei ATCC334 intervention. Conclusion These results highlight that medium and high doses of L. casei ATCC334 alleviate radiation‐induced intestinal damage by enhancing the mucosal barrier and remodeling the gut microbiota structure and metabolic activity.