Fufang-Xialian-Capsule (FXL) is a traditional Chinese medicine (TCM) formula which was utilized to treat chronic atrophic gastritis. Despite the chemical constituents have been clarifying by our previous studies, but the metabolism of FXL after oral was still unclear. In order to clarify the mechanism of these absorbed components, a target-group-change (TGC) strategy was utilized to analysis the collected data. This strategy include five steps: (1) acquired the mass spectra data and tandem mass spectra data simultaneously; (2) confirmed the prototype absorbed into blood and the tandem mass behavior of prototype; (3) clarified the potential group change of prototypes after metabolism by Metabolynx XS software; (4) confirmed the target group change acquired by compare the tandem mass behavior of metabolites with their prototypes; and (5) inferred the position of group change occurred and metabolic pathways of each prototypes. Based on the TGC strategy, the structure of metabolites and the metabolic pathways of FXL were confirmed. The main group change behaviors on the prototypes after metabolism include demethylation, methylation, hydroxylation and glucuronide conjugation. As the results, there were 34 metabolites transformed from 11 prototypes confirmed, these 11 prototypes include 4 flavones, 5 alkaloids and 2 ginsenosides. All the metabolites could be identified or tentatively characterized according to the structure of metabolites and previous reports.