Aquaporin-3 (AQP3) is expressed in various parts of the intestine, where it regulates the proliferation and migration of intestinal epithelial cells and the transport of glycerol and hydrogen peroxide. Our study aimed to investigate the effect on the expression of AQP3 of intestinal injury in septic mice and whether oral administration of glycerol can reduce intestinal epithelial injury and barrier disorder by acting as a partial substitute for the function of AQP3. We established a sepsis model by cecal ligation and perforation (CLP) in mice. Sepsis induced intestinal injury, as demonstrated by the disordered destruction of the morphology of the intestinal mucosa, time-dependent increases in Chiu’s score ( p < 0.05), significantly increased ( p < 0.05) plasma concentrations of determination of the levels of diamine oxidase (DAO) and intestinal fatty acid-binding protein 2 (FABP2), and time-dependent downregulation of the expression of AQP3 and occluding ( p < 0.05). While the administration of oral glycerol partially ameliorated the sepsis-induced injury of the intestinal mucosa, as shown by the partial recovery of the morphological structure, with decreased Chiu’s score, decreased plasma concentrations of DAO and intestinal-type FABP2, upregulated expression of occludin and decreased mortality rate (Sepsis vs. Sepsis + Glycerol, p < 0.05). The results showed that the expression levels of AQP3 and occludin were downregulated after septic intestinal injury, while treatment with glycerol, which acts as a substitute for AQP3, partly ameliorated intestinal injury and improved the survival rate. This preliminary experiment suggests that AQP3 may protect the intestinal tract against the effects of sepsis.