Microreactor technology shows great potential in the enhancement of liquid–liquid mass transfer, which is important especially when highly viscous fluids are involved. This provides an attractive way to intensify the extractive desulfurization (EDS) using ionic liquids (ILs) as an effective technique for ultralow-sulfur diesel production. This work concerns the extraction of dibenzothiophene in model diesel by [BMIM]PF6 in a microchannel. The effects of the phase ratio and temperature on the hydrodynamics and mass transfer characteristics were investigated systematically. Higher temperature is beneficial for forming stable slug flow and droplet flow, as well as for increasing the overall mass transfer coefficient. The contributions of mass transfer during the droplet moving and forming stages were also discussed. Considerable mass transfer contribution (9–64% of the whole) was found during the droplet forming stage, and the mass transfer coefficient during the droplet moving stage can be well predicted by a two-film model.