Gandou decoction (GDD), a well-known traditional Chinese medicine (TCM) formula, has been widely used for decades to treat Wilson's disease (WD) in China due to its remarkable clinical effects. However, the chemical constituents of GDD still remain unclear because of their complexity. In this work, a reliable and sensitive strategy based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS^E) and UNIFI informatics platform was applied to investigate the chemical components in GDD. In total, 96 compounds including anthraquinones, alkaloids, protostane triterpenoids, flavonoids, triterpenoid saponins, tannins, curcuminoids, etc, were identified or tentatively characterized from GDD by comparing their retention time, accurate mass within 5 ppm error and MS^E fragmentation patterns. Among them, eleven compounds were confirmed unambiguously with reference standards. Representative compounds in different chemical structure types were analyzed in fragmentation patterns and characteristic ions. Moreover, to better understand the chemical contribution of individual herbs to the whole decoction, the corresponding each herb in GDD was also detected. This study developed a rapid method for characterizing the chemical constituents in GDD, which could not only be used for chemical standardization and quality control, but also be helpful for further research of GDD in vivo.