Compound Rhubarb Enema (CRE) is a classic formula comprised of Rhubarb and Prunus mume in a weight ratio of 5:1 for the treatment of severe hepatitis and chronic kidney disease. High-performance liquid chromatography (HPLC) and micellar electrokinetic chromatography (MEKC) were compared to simultaneously determine and separate five anthraquinones in CRE. An ultraviolet detector at 254 nm with an isocratic elution of methanol and 10% H3PO4 in water (84:16) at 30°C in HPLC effectively detected this separation in 25 min. In addition, separation is performed by using an electrolyte consisting of 25 mM sodium tetraborate, 4 mM sulfobutylether-β-CD (SBE-β-CD), 20 mM sodium dodecyl sulfonate (SDS), and 2% methanol at pH 10.1 and at a separation voltage of 20 kV in 18 min. The detection limits of anthraquinones were 0.04-0.08 μg mL^-1 and 0.4-0.8 μg mL^-1 for the HPLC and MEKC methods, respectively. Two methods were evaluated and compared with a number of validation characteristics (repeatability, precision, calibration range, and recovery). The established HPLC and capillary electrophoresis (CE) methods are suitable for quantitative determination of the five components in CRE.