In this study, two kinds of amine-based protic ionic liquids (PILs), namely, 2-[2-(dimethylamino)ethoxy] ethanol propionate ([DMEE][CO2Et]) and 3-(dimethylamino)-propanenitrile propionate ([DMAPN][CO2Et]), were introduced into the desulfurization process for the first time. Some important parameters, such as stirring speed, ionic liquid (IL) dosage, initial concentration, etc., were investigated. According to the experiments, the sulfur content in the model oil can be effectively removed from 1600 to about 650 ppm by a single extraction cycle. After five cycles, the sulfur content could reach up to 19 ppm and the deep desulfurization was achieved. Most important, the recycling of PILs was realized by vacuumed distillation. The properties and extraction efficiency of PILs have no change after recycling. At the same time, the extraction mechanisms were probed. The results show that the hydrogen bond formed between the sulfur of dibenzothiophene (DBT) and the active hydrogen of PIL accounts for the high desulfurization efficiencies. This novel process would provide a new route for extraction desulfurization of diesel fuels.