Ionic liquids (ILs) are promising solvents for separating aromatics from fuel oils. However, studies for separate polycyclic aromatics with ILs are rare and insufficient, and the impact of solute structure on extraction performance still needs to be determined. In this work, we use 1‐ethyl‐3‐methylimidazolium bis([trifluoromethyl]sulfonyl)imide ([EMIM][NTF2]) as an extractant to separate 1‐methylnaphthalene, quinoline, and benzothiophene from dodecane mixtures. Liquid–liquid equilibrium experiments identified the optimal operating conditions. Nine solute molecules, including five alkanes and four aromatic hydrocarbons, were used to study the relationship between extraction performance and solute structure. Molecular dynamics simulation and quantum chemistry calculations gave a deep insight and reasonable interpretation of the structure‐performance relationship at the molecular level. An industrial‐scale extraction process was proposed. The IL can be easily regenerated using heptane as a back‐extractive solvent. A high‐purity fuel oil with aromatic content below 0.5 wt% is obtained after 8‐stage extraction.