Objective: This study aims to systematically explore the mechanism of Dahuang Mudan Decoction in treating inflammatory bowel disease through metabolomic analysis, revealing its therapeutic effects and potential pathways in mice, and providing a scientific basis for clinical treatment. Methods: An acute colitis model in mice was established by administering dextran sodium sulfate (DSS) in drinking water continuously for 7 days. After successful modeling, the mice were randomly divided into an ulcerative colitis model group, a mesalazine group, and low-, medium-, and high-dose Dahuang Mudan Decoction groups. The intervention was administered via continuous gavage for 7 days. Body weight changes and colon length were recorded, and the disease activity index (DAI) and fecal occult blood status were monitored. Colon length was measured, and colon tissue was subjected to HE staining and pathological scoring to assess inflammatory damage. Intestinal tissue samples were collected for metabolomic analysis to screen for differential metabolites and perform pathway enrichment analysis. Results: The experimental results indicated that, compared with the model group, intervention with Dahuang Mudan Decoction significantly improved the colitis phenotype induced by DSS, as evidenced by alleviated weight loss, reduced DAI scores, decreased colon shortening, and mitigated histopathological damage, along with improved inflammatory cell infiltration and crypt structure destruction. Metabolomic analysis revealed a clear separation in metabolic profiles between the model and normal groups. Conclusion: Dahuang Mudan Decoction induced a holistic shift in the metabolic phenotype of the model mice, partially reverting/remodeling it toward the normal state.