In propyl propionate production, methanol-methyl propionate azeotropes form at the column top, complicating conventional distillation separation. This work explores the process of extraction distillation for separating methanol-methyl propionate azeotropes using ionic liquids (ILs) from three aspects: molecular structure information, separation feasibility, and clean process design and optimization. In terms of molecular structure information, the separation ability of 27 cations and 28 anions for methanol-methyl propionate azeotropes is investigated using density functional theory, evaluating the value size, bonding type, and strength both quantitatively and qualitatively. In terms of separation feasibility, COSMOthermX software predicts the vapor−liquid equilibrium data of methanol-methyl propionate-ILs at 101.3 kPa, exploring the effects of IL concentration and type on alcohol/ester azeotrope separation, at the same time, the prediction results and performance were verified by experiments. In terms of process design and optimization, simulation processes for using ILs to separate alcohol/ester azeotropes have been established. The final product purity reaches over 99.99%, with a maximum reduction of 16.08% and 33.84% in total annual costs and gas emissions.