A rapid method for the simultaneous determination of berberine (BBR), matrine (MT) and oxymatrine (OMT) by nonaqueous capillary electrophoresis (NACE) was developed. Optimum separation of the analytes was obtained on a 50cm×50μm i.d. fused-silica capillary using a non-aqueous buffer system of 70mM ammonium acetate, 7.0% acetic acid and 10% acetonitrile at 25kV and 20℃. The relative standard deviations (R.S.D.) of the migration times and peak areas of the three active components were 0.06%-0.20% and 0.12%-3.41% for berberine, 0.11%-0.60% and 0.74%-1.63% for matrine, 0.15% and 0.45% for oxymatrine, respectively. Detection limits of berberine, matrine and oxymtrine were 0.18μg/mL, 4.08μg/mL and 4.16μg/mL, respectively. In the tested concentration range, good linear relationships (0.9992 for berberine, 0.9988 for matrine and 0.9988 for oxymatrine) were observed. The linear calibration ranges were 0.45-360.0μg/mL for berberine, 8.16-408.0μg/mL for matrine and 20.8-416.0μg/mL for oxymatrine. This method has been successfully applied to the phytochemical analysis of alkaloids extracts from two commonly used traditional Chinese herbal drugs: Sophora flavescens Ait. (Kushen) and Cortex phellodendri chinensis (Huangbai) and their medicinal preparations.