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The technologies of ionic-liquid-mediated extraction have shown the good prospects for replacing traditional methods for separating natural bioactive homologues. However, so far, the roles and interactions of the anions and cations in the extraction process are not clear, which seriously hinders the further exploration of this new extraction technology. In this work, we report a detailed computational study, combined with experiment, on the interactions and hydrogen bonds between 1-butyl-3-methylimidazlium hexafluorophosphate ([Bmim][PF6]) ionic liquid (IL) and natural bioactive homologues, namely, three soybean isoflavone aglycones as model compounds. The distribution coefficients, D, of the three aglycones were experimentally determined in the [Bmim][PF6]–water biphasic system, and the order was found to be genistein (182.6) > daidzein (51.4) > glycitein (41.9). In DFT calculations, the lowest-energy complexes were obtained, and it was found that H-bonds are explicit intermolecular interactions in these complexes and that the IL can recognize these similar homologues by forming different H-bonds with the phenolic hydroxyls of aglycones. Furthermore, we found that the anions play a more important role in recognition than the cations. Subsequently, results of molecular dynamics (MD) simulations exhibited a good match with the structures of the isolated complexes calculated by DFT and also discovered that H-bonds were the main interactions between the anions and the phenolic hydroxyls in the first solvation shell.