High-speed counter-current chromatography methods, combined with solvent partition, were applied to the systematic separation and purification of chemical components from Chinese medicinal herb Polygonum multiflorum extract. The aim of this paper is summing up the rules of solvent system selection for diverse fractions of herbal extract, and establishing the systematic pattern to screen the bioactive constituents rapidly. Nine compounds including emodin, chrysophanol, rhein, 6-OH-emodin, emodin-8-beta-D-glucoside, polygonimitin B, 2,3,5,4'-tetrahydroxystilbene-2-beta-D-glucoside, gallic acid and an unknown glycoside, which differed in quantity and polarity remarkably, were obtained. The purities of them were all above 97% as determined by high-performance liquid chromatography (HPLC), and their structures were identified by 1H NMR and electrospray ionization mass spectrometry (ESI-MS). The results demonstrated that HSCCC is a speedy and efficient technique for systematic isolation of bioactive components from traditional medicinal herbs.