To improve the quality of fluid catalytic cracking (FCC) diesel, ionic liquids (ILs) were used as promising neoteric solvents to extract bicyclic S/N-compounds (quinoline and 1-benzothiophene) from FCC model oil. In addition to the thermodynamic properties, including solvent capacity and selectivity, physical properties such as viscosity and thermal stability are also considered as important factors in the IL screening process. 1-Ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C2MIM][NTF2]) was selected as the most suitable extraction solvent by the COSMO-RS model, and the accuracy of this model was verified based on the collected experimental data. Liquid–liquid equilibrium experiments were performed to study the effects of the initial quinoline and 1-benzothiophene concentrations, mass solvent ratio, extraction stages, and the presence of other aromatics on the extraction efficiency. Then, the extraction mechanism and the differences in the extraction effects for the quinoline and 1-benzothiophene systems were explored by quantum chemical calculation and molecular dynamics simulation. The consistency between experiments and theoretical calculation indicates that the electrostatic interaction is the main reason for the difference in the extraction efficiency between the quinoline and 1-benzothiophene systems.