A silver ion high-speed counter-current chromatography ([Ag+]-HSCCC) was developed to separate and purify five sesquiterpenoids from germacrene A fermentation broth. The solvent system was consisted of n-hexane-methanol-silver nitrate (3 mol/L) solution (10:9.5:0.5, v/v). By employing this chromatographic protocol, five sesquiterpenoids named β-elemene (1; 54.1 mg), germacrene A (2; 28.5 mg), γ-selinene (3; 4.6 mg), β-selinene (4; 3.4 mg), and α-selinene (5; 1.3 mg) were obtained successfully from 500 mg extracted crude sample with purities of 97.1%, 95.2%, 98.2%, 96.3% and 98.5%, respectively, combined with preparative HPLC. The results reveal that the addition of metal ion in biphasic solvent system significantly improved the HSCCC separation factor of sesquiterpenoids. Meanwhile, our study also provided an alternate approach to separate the compounds with less polarity, also geometrical isomers and various natural product classes.