The electro-polymerization desulfurization process is a promising technology for oil desulfurization. However, using ionic liquids as electrolytes for exploring deep desulfurization through the electro-polymerization method has not yet been well studied. In this study, four imidazole nitrate ionic liquids were successfully synthesized using a typical two-step method and characterized by H-NMR and TGA element analysis. Then, the electro-polymerization desulfurization experiment is conducted using thiophene as model oil and the ionic liquid [Cmim][NO] as electrolyte. The effects of the oil-agent ratio, electro-polymerization potential, temperature, and reaction time on the desulfurization rate were invested. The results showed that the maximum desulfurization rate of the ionic liquid [Cmim][NO] reached 68.7% under the optimal conditions: oil-agent ratio of 3 : 1 (mL), electro-polymerization potential of 2.5 V, temperature of 80 °C, and reaction time of 150 min. Moreover, the effects of temperature and reaction time on the desulfurization performance of the imidazole nitrate ionic liquid homologs [C mim][NO] ( = 2, 3, 6) were also explored. The results showed that extending the time or increasing the temperature can enhance desulfurization. Finally, the electrochemical desulfurization mechanism and the desulfurization performance of the real oil were further investigated, with a maximum desulfurization rate of 51.2%. The desulfurization rate of ionic liquid can reach 55.1% after five cycles. This study is of great significance for further study of electrochemical desulfurization and promoting clean oil production.