Gui-Zhi-Jia-Ge-Gen-Tang (GZJGGT) is a traditional Chinese medicine (TCM) prescription commonly used to treat cervical spondylopathy, scapulohumeral periarthritis, etc. Though it is widely applied in clinical practice, the effective constituents of GZJGGT remain unclear. This was the first report on the identification of the chemical constituents from GZJGGT in vitro and in vivo using LC-IT-MS combined with LC-Q-TOF-MS. A total of 141 constituents were detected in GZJGGT, and 77 were identified. These compounds mainly included flavonoid glycosides, triterpene saponins, monoterpene glycosides, puerosides, and organic acids. Among them, 12 compounds were unequivocally identified in comparison with reference substances. Additionally, a diagnostic base peak ion filtering strategy for rapid classification of flavonoid O-glycosides and C-glycosides was proposed. After gastrointestinal administration of GZJGGT to rats, 45 prototypes and 48 metabolites in rat plasma were speculated. In addition, the metabolic profile of GZJGGT was portrayed to understand interrelationship between metabolites.