In the process of producing low-carbon alcohols from coal, azeotropic waste containing ethanol and n-hexane is generated. To prevent environmental risks and resource waste from solvent loss, this study selected green solvent ionic liquids (ILs) for their separation. First, we screened five anions with high selectivity based on the conductor-like screening model for realistic solvents (COSMO-RS), and through various quantum chemical calculations, we found that the anions play a significant role in the separation of the two components, with [HSO4]− showing the best separation performance. Second, we predicted the phase equilibrium data for ILs containing [HSO4] − in the azeotropic system, considering practical factors such as price and viscosity, and selected [EMIM][HSO4], [BMIM][HSO4], and [HMIM][HSO4] for experiments. The results indicated that simpler cation side chains enhance the separation capability of the system. Then, a toxicity analysis of the ILs ensured their biocompatibility and feasibility. Finally, we established the extraction distillation process and visualized the interactions between the ILs and the azeotropic system through molecular dynamics simulations. This work provides theoretical guidance for the separation of alcohols and alkanes in the industry.