1. Huang–Lian–Jie–Du Decoction (HLJDD) is widely used for the treatment of hypertension, diabetes, inflammation and neural system diseases in clinic. In the present study, the comprehensive metabolic profile of HLJDD was demonstrated reliably and rapidly followed by the metabolic pathway analysis of six typical pure compounds (four alkaloids, one flavonoid and one iridoid) in HLJDD using LC–IT-MS combined with high resolution LC–FT-ICR-MS. 2. Totally, 85 compounds, including 32 prototype components and 53 biotransformed metabolites were detected and characterized in the urine and feces after oral administration of HLJDD and six pure compounds to rats, respectively. Among them, 17 prototypes were identified definitely with standard references. 3. Hydroxylation, demethylation and glucuronidation reactions of alkaloids, as well as glucuronidation and sulfonation reactions of iridoids and flavonoids, were observed as the major metabolic pathways of HLJDD. Flavonoids, iridoids and their metabolites were mainly excreted from urine. However, amount of alkaloids were detected in feces. 4. In general, the distinctive metabolic process of three kinds of representative components in HLJDD was clarified. The in vivo metabolic network of HLJDD was demonstrated. Meanwhile, the investigation of representative pure compounds in metabolic study provided a valuable strategy to elucidate the full-scale metabolic fate of HLJDD. This might