A nitrogen-containing ionic liquid was synthesized using an aromatic nitrogen-containing heterocyclic and an amino acid, and applied to the extractive desulfurization process to remove benzothiophene, dibenzothiophene, and 4,6-dimethyldibenzothiphene from a model fuel oil. Chemical characterizations and simulation using Gaussian 09 software confirmed the rationality of an ionic liquid structure. Classification of non-covalent interactions between the ionic liquid and the three sulfur-containing contaminants was studied by reduced density gradient analysis. The viscosity of the ionic liquid was adjusted by addition of polyethylene glycol. Under extraction conditions of the volume of ionic liquid to oil as 1:1 and temperature as room temperature, the desulfurization selectivity of ionic liquid followed the order of 4,6-dimethyldibenzothiphene (15 min) < benzothiophene (15 min) ≈ dibenzothiophene (10 min). Addition of p-xylene and cyclohexene to the fuel oil had little effect. The extractant remained stable and effective after multiple regeneration cycles.