An efficient method for purification of alkaloids from Corydalis yanhusuo W. T. Wang using HPLC was developed, featuring a polar-copolymerized stationary phase named C18HCE. As ionizable solutes, the crude alkaloid sample often suffered from serious peak tailing problem on conventional RP-LC columns, and the separation would rapidly became destroyed with the increasing of load amount. However, on the new stationary phase, good peak shapes (asymmetry factor1.5) as well as good loadability were easily obtained in a commonly used acidic mobile phase condition. The loading amount could reach 10 mg per injection on an analytical C18HCE column for laboratory-scale purification. About 6.8 mg of palmatine (HPLC purity98%) and 44.4 mg of dehydrocorydaline (HPLC purity98%) were rapidly derived from 200 mg of the crude alkaloid sample, and the recoveries of these two compounds were 76.5 and 81.7%, respectively. The purified alkaloids were characterized by comparing retention times with standard compounds as well as (1)H-NMR data. The new method is simple and high yielding, and it may provide a promising tool for purification of alkaloids as well as other alkaline compounds.