In order to utilize and control the invasive weed, bioactive compounds from essential oil of Flaveria bidentis (L.) Kuntze were studied. Steam distillation extraction and one step high-speed counter-current chromatography were applied to separate and purify the caryophyllene oxide, 7,11-dimethyl-3-methylene-1,6,10-dodecatriene, and caryophyllene from essential oil of Flaveria bidentis (L.) Kuntze. The two-phase solvent system containing n-hexane/acetonitrile/ethanol (5:4:3, v/v/v) was selected for the one step separation mode according to the partition coefficient values (K) of the target compounds and the separation factor (α). The purity of each isolated fraction after a single high-speed counter-current chromatography run was determined by high performance liquid chromatography. A 3.2 mg of caryophyllene oxide at a purity of 92.6%, 10.4 mg of 7,11-dimethyl-3-methylene-1,6,10-dodecatriene at a purity of 99.1% and 5.7 mg of caryophyllene at a purity of 98.8% were obtained from 200 mg essential oil of Flaveria bidentis (L.) Kuntze. The chemical structures of these components were identified by GC-MS, (1) H-NMR, and (13) C-NMR.