A method for preparative purification of loganin and morroniside from Fructus corni was established by combination of macroporous absorption resin column separation and high-speed counter-current chromatography (HSCCC). The crude extracts obtained from Fructus corni by ultrasonic extraction with 50% methanol were subjected to separation on a macroporous resin column and then eluted with 15% and 40% ethanol, respectively. A fraction of 40% ethanol was used as the sample for separation of morroniside and loganin by HSCCC. The two-phase solvent system used for HSCCC separation was n-butanol—methanol—1% acetic acid water (4:1:6, v/v). The upper phase was used as the stationary phase of HSCCC. Morroniside (28.7 mg) of 97.8% purity and loganin (11.5 mg) of 98.6% purity were obtained in a one-step HSCCC separation from 50 mg of sample. The structures of morroniside and loganin were identified by ¹H-NMR and ¹³C-NMR.