Berberine is one of the most important bioactive compounds used in Chinese herbal drugs to evaluate the quality of the Phellodendron cortex. The cortices of Phellodendron wilsonii and Phellodendron amurense, extracted by using a microwave-assisted process under a domestic microwave oven in methanol solvent and analyzed by capillary electrophoresis with the buffer solution of 82% 0.1 M aqueous sodium acetate and 18% MeOH (v/v), were demonstrated to be higher in extracting berberine contents and shorter in the process time than those extracted by using a reflux extraction in methanol solvent (for sample B, 2.27 ± 0.08% in 3 min vs. 1.92 ± 0.14% in 5 hrs, respectively). Therefore, the microwave-assisted process for extraction of berberine is more efficient, rapid and convenient than the reflux extraction and can be used for the extraction of bioactive substances from the crude Chinese drugs.