Achieving strong interaction with the targeted composition and constructing abundant transport channels is crucial to obtain the pervaporation (PV) membrane with high selectivity and flux. Here, three ionic liquids (ILs) were screened out based on their relative selectivity and capacity targeting for bioethanol dehydration by COSMO-RS. The interaction energies analysis between ILs, EtOH, and H2O suggests that the ILs can form strong hydrogen bonds with water and disrupt the hydrogen bond in the EtOH–H2O azeotropic mixture, which is beneficial for improving the selectivity. Furthermore, driven by the multiple hydrogen bonds, electrostatic interactions, and van der Waals forces, ILs could self-assemble with polyvinyl alcohol (PVA) to fabricate the PV membrane with well-ordered micelle nanostructure, as its structure was revealed by MD simulations. The formation of the ILs-PVA micelle dramatically influenced membrane surface morphology, roughness, and water contact angle, providing an extra transport channel for the membrane. The optimal membrane (at the cmc point) exhibited a superior ethanol dehydration separation factor of 1627, along with a flux of 684 g/m2h at 50 °C. It can be expected that this novel self-assembled ILs-PVA micelle nanostructure strategy will find promising applications in other azeotropic mixture separation processes, like ethanol-ethyl acetate, water-butanol, etc.