Desulfurization of diesel using 1-ethyl-3-methylimidazolium diethyl phosphate in a lab-scale extractive column was investigated to explore a deep desulfurization process that could be used as a supplemental technology to hydrodesulfurization. The results showed that the dibenzothiophene derivatives could be removed by extraction with 1-ethyl-3-methylimidazolium diethyl phosphate, the extraction sulfur-containing components increase with the mass ratio of 1-ethyl-3-methylimidazolium diethyl phosphate to diesel, and lower viscosity could also result in the higher desulfurization result. Optimum feed rate and an appropriate extraction temperature were needed to ensure the desulfurization effect. Extraction yield of sulfur-containing compounds followed the order of C-2-DBT > DBT > C-1-DBT > 4-MDBT > 4,6-DMDBT > -C-2-BT > C-2-BT > C-3-BT.