A β-cyclodextrin (β-CD) and ionic liquid (1-ethyl-3-methylimidazolium tetrafluroborate, 1E-3MI-TFB) modified capillary zone electrophoretic (CZE) method has been developed to determine three flavonoids (genkwanin, apigenin and luteolin) in Flos Genkwa with 4-methylumbelliferone as internal standard. The effects of buffer pH and concentration, β-CD concentration and ionic liquid on separation were investigated. The optimum electrophoretic conditions are as follows: 20 mmol·L-1 tetraborate (pH 9.0)- 6 mmol·L-1 β-cyclodextrin-0.04 %  1E-3MI-TFB (V/V) as the running buffer, applied voltage of 25 kV. Under the optimized conditions, the calibration curves of the three flavonoids all showed excellent linearity in the 1~100 mg· mL-1 range. The relative standard deviation in migration time and peak area was 0.21 % and 2.92 % for genkwanin, 0.15 % and 2.33 % for apigenin, 0.28 % and 3.35 % for luteolin. The detection limits of the three flavonoids ranged from 0.26 to 0.32 mg?mL-1. The recoveries of the three flavonoids ranged between 94.3 % and 103.5 %