Deep desulfurization of fuels has attracted worldwide attention as a result of environmental concerns. In this study, a new series of protic ionic liquids (PILs) with different acidic anions were synthesized and the extraction desulfurization of dibenzothiophene (DBT), benzothiophene (BT), and 4,6-dimethyldibenzothiophene (DMDBT) in model oil was carried out. The result showed that the extraction efficiency of DBT decreased in the order of [1,8-diazabicyclo[5.4.0]undec-7-ene] ([DBU]) > [N-formylmorpholine] ([NFM]) > [N-methylimidazole] ([HMIM]) > [N-methylmorpholine] ([NMM]) while the PIL anion was formate and DBU-based PILs with different anions could remove more than 80% DBT and BT in 1 cycle. The extraction efficiencies of [DBU]Pr were 98.33% for DBT (from 500 to 8.35 ppm) and 98.67% for BT (from 500 to 6.65 ppm) after 3 extraction cycles. The value for DMDBT was 99.38% (from 500 to 3.10 ppm) after 5 cycles. The interaction energies of these PILs with three aromatic sulfur compounds were also studied through quantum chemistry calculation. Finally, the regeneration of the used PIL was performed by the back -extraction method and checked by H-1 nuclear magnetic resonance.