Two new prenylated flavonoids, sinoflavonoids A-B, were isolated from the dried fruits of Sinopodophyllum emodi by silica gel column chromatography (SGCC) and high-speed counter-current chromatography (HSCCC). The 95% ethanol extract was partitioned with petroleum ether, dichloromethane, ethyl acetate, and n-butanol in water, respectively. The ethyl acetate fraction was pre-separated by SGCC with a petroleum ether-acetone gradient. The eluates containing target compounds were further separated by HSCCC with n-hexane-ethyl acetate-methanol-water (4:6:4:4, v/v). Finally, 17.3mg of sinoflavonoid A and 25.9mg of sinoflavonoid B were obtained from 100mg of the pretreated concentrate. The purities of sinoflavonoid A and sinoflavonoid B were 98.47% and 99.38%, respectively, as determined by HPLC. Their structures were elucidated on the basis of spectroscopic evidences (HR-ESI-MS, (1)H-NMR, (13)C-NMR, HSQC, HMBC). The separation procedures proved to be efficient, especially for trace prenylated flavonoids.