Shidan granule (SDG), a traditional Chinese medicine in‐hospital preparation, has been demonstrated to exert good effects on chronic atrophic gastritis (CAG) in clinics. However, the underlying mechanism of SDG against CAG is still unclear. This study utilized an untargeted plasma metabolomics approach to explore the potential mechanism of SDG in CAG rats using LC–MS and pattern recognition analysis. The results indicated that SDG could effectively improve the biochemical indexes and pathology features of CAG rats. Nineteen potential biomarkers (variable importance in projection > 1 and P < 0.05) contributing to CAG progress were identified. After SDG intervention, 17 biomarkers were obviously restored to normal levels. Further metabolic pathway analysis showed that aspartate and glutamate metabolism, arachidonic acid metabolism, arginine and proline metabolism, and TCA cycle were the most related pathways for SDG treatment. Based on these findings, the main mechanisms of SDG against CAG might be attributed to the regulatory effects of energy balance, inflammatory suppression, and improvement in disturbed amino acid and lipid metabolism. This study provided information for the mechanism research of SDG against CAG and would promote its clinical application.