The Maillard reaction (MR) is inevitable in food processing and daily cooking, but whether the MR degree would affect the biological activity of the protein in vivo remains unknown. In this study, we used untargeted metabolomics techniques to explore the effects of two different levels of Maillard reaction products (MRPs) of ovalbumin (OVA) on metabolites in colitis mice. Studies have shown that MR could affect protein metabolites in vivo and MRPs of OVA could reduce the concentrations of IL-6 and IL-1β and intestinal permeability. Metabolomics results showed that the degree of MR affected the abundance of oligopeptides and bile acids in vivo. This study revealed that MRPs could regulate the abundance of metabolites such as taurocholic acid and putrescine, and repair the intestinal barrier in colitis mice through signaling pathways such as secondary bile acid biosynthesis, bile secretion and ABC transporters. The investigation has significant implications for the digestion properties and metabolite regulation of MRPs in vivo, and also promotes the application of MRPs in functional foods.