The intestinal mucosa is the intestinal lumen tissue that protects the intestine from invasion, maintains intestinal barrier function, and participates in the immune response. Diseases such as inflammatory enteritis and intestinal infections can cause damage to the intestinal mucosal barrier and dysfunction. The aim of this study was to investigate the improvement mechanism of malvidin-3-O-galactoside (M3G) on small intestinal mucosal barrier function. C57BL/6J male mice were given dextran sodium sulfate (DSS) for 7 days to induce enteritis, and then were fed normally with or without M3G supplementation for another 7 days. The results showed that M3G supplementation significantly improved the disease activity index (DAI) score and small intestinal tissue injury in mice with DSS induced enteritis. M3G ameliorated the small intestinal mucosal mechanical barrier function by modulating the expression of mucin 2 (MUC2), zona occludens 1 (ZO-1), Occludin, Claudin-1, intestinal fatty acid binding protein (iFABP), and trefoil factor 3 (TFF3) in the small intestine mucosa, and the serum levels of D-lactic acid (D-LA), lipopolysaccharide (LPS), and diamine oxidase (DAO) were significantly decreased. Additionally, M3G also relieved the small intestinal immunologic barrier of mice by decreasing the immune protein levels of immunoglobulin A (IgA), immunoglobulin M (IgM), and immunoglobulin G (IgG) in serum, and secretory immunoglobulin A (SIgA) level in small intestine tissue. Furthermore, M3G inhibited the expression of Notch pathway-related proteins such as Notch1, Notch intracellular domain (NICD), delta-like ligand 4 (DLL4), delta-like ligand 1 (DLL1), and hairy/enhancer of split 1 (Hes1). In conclusion, the results demonstrated that M3G can improve intestinal mucosal barrier function by inhibiting Notch pathway.