In this study, an ultra-performance liquid chromatography/photo-diode-array/quadrupole time-of-flight mass spectrometry (UPLC-PDA-QTOFMS) based chemical profiling method was established for rapid global quality evaluation of Radix Paeoniae. By virtue of the high resolution, high speed of UPLC and the accurate mass measurement of TOFMS, a total of 40 components including 29 monoterpene glycosides, 8 galloyl glucoses and 3 phenolic compounds were simultaneously separated within 12 min, and identified through the matching of empirical molecular formulae with those of published components in the in-house library, and were further elucidated by adjusted lower energy collision-induced dissociation (CID) mass spectra. Among forty components, five monoterpene glycoside sulfonates were identified as novel components. The established method was successfully applied to rapidly and globally compare the quality of Radix Paeoniae Alba and Radix Paeoniae Rubra, two post-harvesting handled products of Radix Paeoniae. Together with paeoniflorin sulfonate, five newly assigned monoterpene glycoside sulfonates were characteristic markers to detect non-official sulfur dioxide gas fumigated Radix Paeoniae Alba samples. It could be concluded that UPLC-PDA-QTOFMS based chemical profiling is a powerful approach for the global quality evaluation of Radix Paeoniae as well as other herbal medicines.