Objective: Chronic nonatrophic gastritis (CNG) is the most common digestive disease. In China, Zuojin pill (ZJP) is considered an effective medicine formula for CNG. However, its efficacy and mechanism have never been explored. In order to understand how and why ZJP demonstrates therapeutic effect on CNG, a clinical trial was conducted. Metabolomics was used to explore its deep mechanism.Methods: A total of 14 patients with CNG were recruited from October 2020 to March 2021 (ChiCTR2000040549). The endoscopy and histopathological changes were evaluated as efficacy. Serum samples were prepared and detected by performing widely targeted metabolome using UPLC. Multivariate statistical analysis was conducted to identify potential differential metabolites and signaling pathways. Last, the signal-related inflammatory factors containing COX-2, IL-4, and IL-17 were confirmed via immunohistochemical staining and enzyme-linked immunosorbent assay.Results: ZJP was able to alleviate several indexes of mucosal injury under endoscopy and histology. Erosion and bile reflux, but not red plaques and hemorrhage, were downregulated by ZJP. In addition, it could remarkably alleviate active chronic inflammation. A total of 14 potential metabolites, namely, hypoxanthine, adipic acid, D-ribono-1,4-lactone, L-sepiapterin, imidazoleacetic acid, sebacate, ADP-ribose, 4-hydroxybenzyl alcohol, 11,12-EET, 15-OxoETE, 12-OxoETE, (±)8-HETE, glycyrrhizinate, and DL-aminopimelic acid, were discriminated by metabolomics. Moreover, certain amino acid metabolism got significance during the disease progress and treatment. The related inflammatory factors including COX-2, IL-4, and IL-17 were inhibited by ZJP in both mucosa and serum.Conclusion: All these results indicated that ZJP partially acts as an inflammatory suppressor to regulate comprehensive metabolism disorders. This might be an important mechanism of ZJP in the treatment of CNG.