Radix Polygalae (RP), the dried root of Polygala tenuifolia Willd., is a well-known traditional Chinese medicine to mediate sedative, antipsychotic, cognitive improving, neuroprotective, and anti-inflammatory therapeutic effects on the central nervous system. In this work, ultra high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC/ESI-Q-TOF-MS/MS) was established for the separation and characterization of the chemical constituents in Radix Polygalae and their metabolites in rat plasma and urine after oral administration. Samples were separated on an Agilent Zorbax Eclipse Plus-C18 column (100mm×2.1mm, 1.8μm) with 0.1% formic acid aqueous solution and acetonitrile as the mobile phase under gradient conditions. Overall, 50 compounds were characterized from the RP, 9 of which are to our knowledge reported for the first time. In vivo, 10 components and 2 metabolites were observed in rat plasma, and 27 components and 7 metabolites were detected in rat urine. The results from this work improve our understanding on the chemical constituents of RP and their metabolic profiling.