Abstract OBJECTIVES The intestinal injury during deep hypothermic circulatory arrest (DHCA) is harmful to clinical outcomes. Cold-inducible RNA-binding protein (CIRBP) plays a protective role in hypothermia. The aim of this study was to explore the effects of CIRBP on intestinal barrier during DHCA. METHODS Sprague-Dawley (wild type, n = 13) and knockout of Cirbp (Cirbp−/−, n = 8) rats were used in the model of DHCA. The histomorphology of the epithelial barrier was evaluated by haematoxylin–eosin, Chiu’s scores, Gram's stain and Ki67. The function of the intestinal barrier was evaluated by serum intestinal fatty acid-binding protein, diamine oxidase and d-lactate. The structure of the epithelial barrier, phosphocreatine-creatine kinase system and adenosine triphosphate were assessed in the intestine. RESULTS The expression of CIRBP significantly increased in the intestine during DHCA. Cirbp−/− rats showed obvious destruction of intestinal barrier after DHCA. Chiu’s scores, intestinal fatty acid-binding protein, diamine oxidase and d-lactate significantly increased in the Cirbp−/− group. Ki67 showed that cell proliferation decreased in the Cirbp−/− rats. In the Cirbp−/− group, zonula occludens-1, E-cadherin and occludin levels were significantly decreased, and these proteins either disappeared or redistributed in the monolayer. Besides, Cirbp−/− resulted in decreased levels of creatine kinase B, glycine amidinotransferase, adenosine triphosphate and creatine contents in the intestine, affecting energy metabolism and balance, which is associated with the maintenance of epithelial barrier during acute injury. CONCLUSIONS CIRBP is related to the maintenance of the intestinal epithelial barrier during DHCA, which is expected to be a new target for the prevention of intestinal injury.