Inflammatory bowel disease (IBD) is a chronic disease of unknown etiology with a progressive and destructive course and an increasing incidence worldwide. Dietary peptides have a variety of biological functions and are effective anti-inflammatories and antioxidants, making them a prospective class of material for treating intestinal inflammation. Our study investigated the association between Ile–Arg–Trp (IRW), a dietary oligopeptide, and intestinal microbial changes during the relief of colitis using different concentrations of IRW. We found that IRW can significantly alleviate mouse colonic barrier damage caused by dextran sulphate sodium salt (DSS) and promote intestinal health. The results of microbial community composition showed that the relative abundance of Bacillota and Lactobacillus in the gut microbiota at different concentrations of IRW was significantly increased and that the abundance of Bacteroides was suppressed. Surprisingly, the relative abundance of Odoribacter also received regulation by IRW concentration and had a positive correlation with acetic acid. IRW at 0.02 mg/mL and 0.04 mg/mL significantly altered the abundance of Bacillota, Odoribacter, and Lactobacillus.