A rapid, sensitive and selective UPLC/MS method using LTQ Orbitrap mass spectrometry was established for the analysis and characterization of the main biological components and their metabolites in rat plasma, urine and feces following oral administration of Lithocarpus polystachyus extract. In vivo, 22 flavonoid metabolites were observed in rat plasma, and 13 metabolites were detected in rat urine, whereas just two aglycones of dihydrochalcone (3-hydroxy phloretin and phloretin) could be detected in rat feces. Among these metabolites, one new and a known dihydrochalcone metabolite were isolated and definitely identified. Besides, five dihydrochalcone metabolites were tentatively identified as new compounds. A metabolism study of 3-hydroxyphlorizin and phloridzin was also conducted. Glucuronidation was the main metabolic pathway of phloridzin, whereas glucuronidation and sulfonation were the main metabolic pathway of 3-hydroxyphlorizin. These results provided a basis for evaluating the bioactive components of a complex natural medicine and their mechanisms of actions. (C) 2014 Elsevier B.V. All rights reserved.