In our present study, two groups of xanthones isomers (1-hydroxy-3,5,8-trimethoxyxanthone and 1-hydroxy-3,7,8-trimethoxyxanthone; 1,8-dihydroxy-3,7-dimethoxyxanthone and 1,8-dihydroxy-3,5-dimethanolxanthone) and other two xanthones (3-methoxy-1,5,8-trihydroxyxanthone and 3,5-dimethoxy-1-hydroxyxanthone) were separated from Swertia franchetiana. First, a solvent system composed of petroleum ether/methanol/water (2:1:0.6, v/v) was developed for the liquid-liquid extraction of these xanthones from the crude extract. Then, an efficient method was established for the one-step separation of these six xanthones by high-speed countercurrent chromatography using n-hexane/ethyl acetate/methanol/ethanol/water (HEMEW; 6:4:4:2:4, v/v) as the solvent system. The results showed that liquid-liquid extraction could be well developed for efficient enrichment of target compounds. Additionally, high-speed countercurrent chromatography could be a powerful technology for separation xanthones isomers. It was found ethanol could be a good methanol substitute when the HEMEW system could not provide good separation factors.