Polygala Radix (PR) is one of the most commonly used traditional Chinese medicines (TCM), but its effective materials are still not very clear. In order to solve the existing problems, the chemical and intestinal metabolic profiles of PR were analyzed via intestinal bacteria incubation model. An integrated analysis method combined ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS) method and ultra-high performance liquid chromatography with ion-trap multi-stage tandem mass spectrometry (UHPLC-IT-MSn) method was established. As a result, a total of 115 polygala compounds were identified from the PR extract. Moreover, 44 metabolites via intestinal microflora were characterized, of which three compounds were formed from xanthone C-glycosides, 25 compounds were formed from polygala saponins and 16 compounds were formed from oligosaccharide multi-esters. To our knowledge, the metabolites of the PR via intestinal microflora metabolism, especially polygala saponins, are the first reported in vitro. The obtained results would provide the methodological support for further studying the effective materials of the PR in vivo.