A capillary zone electrophoretic method has been developed for the quantitative analysis of three active comppounds, 12-hydroxy-desmethoxyyangonin (HD), 12-β-d-glucopyranoside-desmethoxyyangonin (GD) and luteolin 3′-(6-E-p-coumaroyl-β-d-glucopyranoside) (LG) in Scorzonera austriaca with UV detection at 254 nm. The applied voltage was 25 kV and the capillary temperature was kept constant at 25 °C. The effect of buffer pH, the concentration of electrolyte and organic modifier on migration were studied systematically. Optimum separation was achieved with 20 mM borate buffer at pH 10.00 containing 10% (v/v) methanol. Daphnetin was used as internal standard for quantification. Regression equations revealed good linear relationship between the ratios of the peak area of each compound and its the ratios of concentration. All the correlation coefficients were higher than 0.9990. The relative standard deviations of migration time and the peak area were <1.46% and 5.13% (inter-day), and <1.65% and 5.16% (intra-day), respectively. The contents of the three compounds in S. austriaca were successfully determined with satisfactory repeatability and recovery.