Separation of high value bioactive compounds is a viable route to make full use of the biomass resources and improve the profitability. However, the sparing aqua- and lipo-solubility of the bioactive compounds makes their separation really challenging. Considering that ionic liquids show good solubility of biomass and could easily form biphasic systems with organic solvents, an ionic liquid (IL)-based biphasic system consisting of ionic liquid, water and ethyl acetate is proposed in this study. Ginkgolide homologues were selected as model compounds to evaluate its practicality. Adequate distribution coefficients, relatively high extraction capacity and selectivity were obtained with the novel biphasic system. The improved distribution coefficients of the ginkgolides are mainly attributed to the multiple interactions between ginkgolide and IL, which were confirmed by means of quantum chemistry calculations. Moreover, the effect of the interactions between ginkgolides and the extraction solvent on the selectivity coefficient was studied by measuring the Kamlet–Taft parameters of the extraction solvent. Based on the results of fractional extraction, which was simulated by calculation and validated by experiments, as well as the comparison of organic solvent consumption, the employed IL-based extraction would be a valid and clean method as an alternative to chromatographic methods for separating bioactive compounds in large-scale operations. It is noteworthy that the amount of organic solvents consumed with this method was supposed to be less than 1/11 of the most widely used chromatographic method.