In this work, a CE method was developed to separate five anthraquinones: aloe-emodin, rhein, emodin, chrysophanol, and physcion. The CE method used a nano-sized metal organic framework MIL-101 (nMIL-101) as pseudostationary phase (PSP) and sorbent for dispersed particle extraction (DPE). The nMIL-101 was synthesized by microwave technique and was characterized by UV-vis, TEM, Zeta potential, X-ray diffraction spectrometry and micropore physisorption. In this method, anthraquinones were adsorbed by nMIL-101 of a fast kinetics within 10 min and then separated by CE. The CE conditions were optimized considering time, pH, buffer ionic strength, and nanoparticles concentration. The optimal CE condition is using 20 mM sodium borate buffer (pH 9.1) containing 15% methanol (v/v) and 400 mg/L nMIL-101 as additives within 8 min. The LODs varied from 24 to 57 g/L, which were lower than those previously reported. Our method has been successfully applied to determine trace anthraquinones in environmental water samples.