A preparative high-speed counter-current chromatography method for separation and purification of liensinine, isoliensinine and neferine from seed embryo of Nelumbo nucifera GAERTN was successfully established by using n-hexane-ethyl acetate-methanol-water (5:8:4:5, v/v, containing 0.5% NH(4)OH) as the two-phase solvent system. From 200 mg of crude extract, 18.4 mg of liensinine, 19.6 mg of isoliensinine and 58.4 mg of neferine were obtained with the purity of 96.8, 95.9, and 98.6%, respectively. The identification of the three alkaloids was performed with (1)H NMR and (13)C NMR.