An ionic liquid ( 1-ethyl-3-methylimidazolium tetrafluoroborate, 1E-3MI-TFB) modified micellar electrokinetic capillary chromatographic ( MEKC) method was developed to separate and determine isoquercitrin, chlorogenic acid and quercetin. The effects of buffer pH and concentration, sodium taurocholate ( STC) concentration and ionic liquid on separation were investigated. The optimum electrophoretic conditions were as follows: 25 mmol/L borax-KH2PO4(pH 9.0)- 40 mmol/L STC-1 parts per thousand 1E-3MI-TFB ( VIV) as the running buffer, applied voltage of 16 kV. Under the optimized conditions, the three analytes were well separated less than 11 min. A good linearity between the peak area and the concentration was observed in the range of 0. 02 - 0. 40 g/L, 0. 02 - 0. 20 g/L and 0. 08 - 0. 60 g/L with correlation coefficients of 0. 9998, 0. 9988 and 0. 9991 for isoquercitrin, chlorogenic acid and quercetin, respectively. The relative standard deviation in peak area and migration time was 2.5% and 1.1% for isoquercitrin, 2. 6% and 1.5% for chlorogenic acid, 3.0% and 1.6% for quercetin. The detection limits (S/N = 3) were 0. 0050 g/L for isoquercitrin, 0. 0045 g/L for chlorogenic acid and 0. 0040 g/L for quercetin. The method was successfully applied to separate and determine isoquercitrin, chlorogenic acid and quercetin in Inula britamica L.