A new method using ultra-performance liquid chromatography (UPLC) in combination with tandem mass spectrometry and a multiple reaction monitoring mode (UPLC-MS/MS-MRM) was developed for simultaneous quantitative determination of anthraquinone derivatives in Radix et Rhizoma Rhei-based medicines. A multi-mode electrospray/chemical ionization (ESCI) and negative ion mode with [M-H]⁻ and its fragments under collision-activated conditions were employed in MS/MS-MRM. The quantitative method was validated and applied to simultaneous determination of anthraquinone derivatives in 21 Radix et Rhizoma Rhei-based medicines. The limits of quantification were in the range of 3.90–9.09 ng mL⁻¹. Average recoveries were between 95.5% and 99.8% with relative standard deviations from 1.8% to 5.3%.