Abstract: To investigate the chemical comparison between decoctions of Radix Paeoniae Rubra and Radix Paeoniae Alba, the samples from legal market were compared using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF MS). Data were statistically analyzed by principal component analysis and orthogonal partial least-squares to latent structures discriminate analysis. The comparing with reference compounds, accurate m/z value analysis of TOF-MS data based on in-house software for automatic tentative identification and QTOF-MS/MS fragment analysis were applied to constituents identification. The results indicate that oxypaeoniflorin and albiflorin are the most important differential constituents in the decoctions of Radix Paeoniae Rubra and Radix Paeoniae Alba, respectively. Moreover, the contents of 8-debenzoylpaeoniflorin, 1’-O-benzoylsucrose, mudanpioside F, mudanpioside C/benzoloxypaeoniflorin, mudanpioside E, (1S,2S,4R)-trans-2-hydroxy-1,8-cineole-B-D-glucopyranoside, saccharose and galloylpaeoniflorin/galloylalbiflorin may also be of significant difference for two kinds of decoctions.