Methane sulfonic acid (MSA) was used as anion to synthesize a series of ionic liquids and its desulfurization performance was evaluated by extraction. The basic physical properties and structural properties of the ionic liquids were evaluated, and it was proved that the ionic liquids could be used and separated well in liquid–liquid extraction desulfurization (EDS) system. The liquid–liquid extraction desulfurization system was enhanced by microchannel technology. The effects of microchannel diameter, extraction temperature, residence time and extraction stage on extraction efficiency were discussed. In the microchannel extraction system, this extraction equilibrium time can be reduced to 60 s from more than 10–15 min or longer in the conventional intermittent extraction techniques, which effectively reduces the synthesis and production cost. This finding may provide some reference for the further study of the micro-reaction technology in the deep removal of sulfur compounds from gasoline by ionic liquid, and further optimize the operating conditions.