“Dogel ebs” was known as Sophora flavescens Ait., a classical traditional Chinese Mongolian herbal medicine, which had the effects on damp‐heat dysentery, scrofula, and syndrome of accumulated dampness toxicity. Although the chemical constituents have been clarified by our previous studies, the metabolic transformation of “Dogel ebs” in vivo was still unclear. To explore the mechanism of “Dogel ebs,” the metabolites in plasma, bile, and urine samples were investigated. A fast positive and negative ion switching technology was used for the simultaneous determination of flavonoids and alkaloids in “Dogel ebs” in a single run. And a target‐group‐change coupled with mass defect filtering strategy was utilized to analyze the collected data. 89 parent compounds and 82 metabolites were characterized by high‐performance liquid chromatography with quadrupole exactive Orbitrap mass spectrometry. Both phase I and phase II metabolites were observed and the metabolic pathways involved in oxidation, demethylation, acetylation, and glucuronidation. 69 metabolites of “Dogel ebs,” including three hydroxyls bonding xanthohumol, formononetin‐7‐O‐glucuronide, 2′‐hydroxyl‐isoxanthohumol decarboxylation metabolite, oxysophocarpine dehydrogen, 9α‐hydroxysophoramine‐O‐glucuronide, etc. were reported for the first time.