Elution-extrusion counter-current chromatography (EECCC) takes full advantages of the liquid nature of the stationary phase. It effectively extends the solute hydrophobicity window that can be studied and renders the CCC technique particularly suitable for rapid analysis of complex samples. In this paper, EECCC was used to screen the crude ethanol extract of Zingiber cassumunar and to isolate milligram-amounts of bioactive components. The two column volume (2V(C)) EECCC method was applied to rapidly optimize the composition of the biphasic liquid system in both reversed- and normal-phase separation mode. With the n-hexane/ethyl acetate/methanol/water 1/1/1/1 (v/v) system, 100mg of crude Z. cassumunar extract were fractionated on a 140 mL-capacity semi-preparative hydrodynamic CCC column and 0.5 g on a 1600 mL column for large-scale preparation. Satisfactory separation efficiency was achieved in both cases, producing milligram-amounts of four phenylbutenoids over 90% pure and of a mixture of diastereoisomers (phenylbutenoid dimers). However, the global throughputs of the two columns were 8 and 11 mg/h, not very different. This is due to the fact that the 1600 mL column could not retain the liquid stationary phase as well as the smaller 140 mL column. It was necessary to work at much lower flow rate than calculated. Methanol was added as a post-column clarifying reagent for stable continuous UV detection. A lipophilic biphasic liquid system composed of n-hexane/acetonitrile/water (5/3/2, v/v) allowed to resolve the pair of diastereoisomers with the larger preparative instrument producing 35 mg of the (+/-)-trans form 99.1% pure and 28 mg of the (+/-)-cis isomer 98.1% pure. Compared with classical elution, the EECCC approach exhibits strong separation efficiency and great potential to be a high-throughput separation technique in the case of complex samples.