A new high-speed counter-current chromatography method for semi-preparative separation and purification of alkaloids from embryo of the seed of Nelumbo nucifera Gaertn was developed by using pH-gradient elution mode. Diethyl ether was used as the stationary phase of the two-phase solvent system and Na(2)HPO(4)/NaH(2)PO(4) buffer solution with pH values of 7.5 and 7.2 in gradient mode as the mobile phase. Consequently, 33 mg of liensinine, 42 mg of isoliensinine, and 67 mg of neferine were obtained from 200 mg of crude extracts. The purities of them were all over 98% as determined by HPLC area normalization method, and the structures were identified by (1)H-NMR and (13)C-NMR.