A high-performance liquid chromatography (HPLC) method has been developed for simultaneous determination of six alkaloids, i.e., (−)-(R)-platydesmin, noroxyhydrastinine, berberine, skimmianine, canthin-6-one, and pteleine in the herbal medicine of Phellodendron amurense Rupr. The optimal condition for extraction and separation was achieved with a linear mobile phase gradient prepared from 0.1% phosphoric acid and acetonitrile. The LODs and LOQs for the analytes ranged from 0.06 to 0.22 μg mL −1 and from 0.25 to 0.80 μg mL −1, respectively. The optimized method was applied to the determination of alkaloids in P. amurense Rupr. and was found to be efficient. This method can provide a scientific and technical platform to the manufacturers for setting up a quality control standard as well as to the public for quality and safety assurance of the proprietary traditional Chinese medicines.