In the maneuver to achieve desulfurization, we have explored various nitro-substituted positional isomeric imidazolium-based aprotic ionic liquids (ILs). Ortho-, meta-, and para-substituted nitro benzyl group-aided imidazolium-based ILs were synthesized and used to understand the extractive desulfurization (EDS) efficiency of fuels. ILs chosen for the experiment were optimized using the B3LYP method and 6-311(++)g(d,p) of Gaussian 09, and their interactions with thiophene derivatives were analyzed using the integrated electric field polar continuum model solvation. Free energy of solvation provided qualitative information about the ability of ILs to achieve desulfurization. Parameters affecting the efficiency of synthesized ILs were perused, such as the effect of IL volume, concentration, duration of rotation, and other such parameters. Lewis acidity, availability of the Lewis acidic site and pi-pi interaction influenced the EDS efficiency of ILs.