A nonaqueous capillary electrophoresis (NACE) method with direct on-column UV detection has been developed for the separation of the pharmaceutically important anthraquinones from the total grass of Xanthophytum attopvensis pierre extract. The separation of three main anthraquinones (1-hydroxy-2-methoxy-3-hydroxymethyl-9, 10-anthraquinone-1-O-β-d-glucoside (1), rubiadin- 1-methylether (2) and 1-methoxy-2-formyl-3-hydroxy-9, 10-anthraquinone (3)) was optimized with respect to concentration of sodium cholate (SC) and acetic acid, addition of acetonitrile (ACN), and applied voltage. Baseline separation was obtained for the three analytes within 5min using a running buffer containing 50mM sodium cholate (SC), 1.0% acetic acid and 40% ACN in methanol. The method of NACE for the separation and determination of bioactive ingredient in traditional Chinese medicines was discussed.