Tripterygium wilfordii (T. wilfordii) and Tripterygium hypoglaucum (T. hypoglaucum), two commonly used Chinese herbal medicines derived from Tripterygium genus, have been widely used for the treatment of rheumatoid arthritis and other related inflammatory diseases in clinical therapy. In the present study, a rapid resolution liquid chromatography/electrospray ionization tandem mass spectrometry (RRLC-ESI-MSn) method has been developed and validated for simultaneous determination of 19 bioactive compounds including four catechins, three sesquiterpene alkaloids, four diterpenoids, and eight triterpenoids in these two similar herbs. The method validation results indicated that the developed method had desirable specificity, linearity, precision and accuracy. Quantitative analysis results showed that there were significant differences in the content of different types of compounds in T. wilfordii and T. hypoglaucum. Moreover, chemometrics methods such as one-way ANOVA, principal component analysis (PCA) and hierarchical clustering analysis (HCA) were performed to compare and discriminate the two Tripterygium herbs based on the quantitative data of analytes, and it was proven straightforward and reliable to differentiate T. wilfordii and T. hypoglaucum samples from different origins. In conclusion, simultaneous quantification of multiple-active component by RRLC-ESI-MSn coupled with chemometrics analysis could be a well-acceptable strategy to compare and evaluate the quality of T. wilfordii and T. hypoglaucum.