In this paper, novel capillary electrophoresis (CE) methods, which used ionic liquids (1-ethyl-3-methylimidazoium tetrafluoroborate, 1-butyl-3-methylimidazoium tetrafluoroborate), were established to separate and determine some bioactive flavone derivatives in Chinese herb Seriphidium santolinum (Schrenk) Poljak. In order to investigate the traits of ionic liquids in CE, borate was also used as electrolyte to compare with. And the excellence of CE, which used ionic liquids as main running electrolyte and beta-cyclodextrin (beta-CD) as modifier, was illuminated as well. As a result of the study, the difference of ionic liquids and borate in CE was discussed and the advantage of CE, which used ionic liquids as electrolytes for separation, was shown. The analysis was obtained within short time (5-6 min). From the result, it was found that the system, which used ionic liquids, was robust because the joule heating was small. The method of CE, which used ionic liquids, has lower detection limits (0.137-0.642 microg/mL) than that of borate (0.762-1.036 microg/mL). And the CE, which used ionic liquids method, has lower limit of linear range (1.100-2.656 microg/mL), while that of CE, which used borate method, was 2.188-5.313 microg/mL.