A novel method was established to separate and quantify simultaneously 11 acidic compounds in traditional Chinese medicine of Conyza blinii levl. and Artemisia annua L. using capillary electrophoresis (CE). Optimized apparatus conditions were given. A fused-silica capillary 50 cm (40 cm to detector)×75 μm i.d. was used.Working voltage of +15 kV was applied at 25 ℃. The buffer(pH=11.42) containing 35.7 mmol phosphate sodium, 2.86×10-5mol/L fluorescein sodium (respondence reagent), and small amount of methanol was used. The hydrodynamic injection of a sample (0.5 psi(3.45 kPa)) during 5 sec was used. Indirect laser induced fluorescence(LIF) detection was applied by LIF detector at wavelength of 488 nm(excitation), 520 nm (detection).The method had a wide linear range, low relative standard deviation, high precision and perfect reproducibility. Real samples assay result was achieved perfectly in this condition.