In this work, an efficient method for preparative separation of procyanidins from raw cacao bean extract by high-speed counter-current chromatography (HSCCC) was developed. Under the optimized solvent system of n-hexane-ethyl acetate-water (1:50:50, v/v/v) with a combination of head-tail and tail-head elution modes, various procyanidins fractions with different polymerization degrees were successfully separated. UPLC, QTOF-MS and 1H NMR analysis verified that these fractions contained monomer up to pentamer respectively. Dimeric procyanidin B2 (purity>86%) could be isolated by HSCCC in a single run. Other individual procyanidins in these fractions could be further isolated and purified by preparative HPLC. The developed HSCCC together with preparative HPLC techniques appeared to be a useful tool for large preparation of different procyanidins from cacao beans. Furthermore, by antioxidant activity assays, it was proved that both fractions and individual procyanidins possessed greater antioxidant activities compared to standard trolox. The antioxidant activities of procyanidins increase as the increase of their polymerization degree.