Ionic liquids were found to be highly selective for extractive removal of aromatic sulfur compounds from fuels at room temperature. The efficiency of ionic liquids for the absorption of aromatic sulfur is dependent on the size and structure of both cations and anions of the ionic liquids. In this work, room temperature H-1, F-19, B-11, and P-31 NMR spectroscopy was used to study the interaction of thiophene as a model aromatic sulfur-containing compound with ionic liquids of 1-n-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6), 1-n-buty-3-methylimidazolium tetrafluoroborate (BMIMBF4), and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIMBF4). The molar ratio of thiophene to each ionic liquid was varied by including saturated absorption of thiophene in ionic liquids. Pronounced changes were observed in NMR chemical shifts of the protons from the imidazolium cations and thiophene (TS), and NMR chemical shifts of fluorine, boron, and phosphorus nuclei of the anions. At the maximum absorption of thiophene in each ionic liquid, the NMR results indicate that a relatively ordered and extended stacking structure of 4/1 TS/BMIMPF6 repeating units was formed in the solution of thiophene and BMIMPF6. Similarly, a stacking structure of 2/1 TS/BMINIBF4 repeating units was formed in the solution of thiophene and BMIMBF4, and a stacking structure of 1/1 TS/EMIMBF4 repeating units was formed in the solution of thiophene and EMIMBF4. NMR results obtained from this study also showed that the chain length or size of the alkyl group on the imidazolium cation and the property and size of the anion determined the absorption capability of thiophene by various ionic liquids with imidazolium cations.