Compared with traditional hydrodesulfurization, new nonhydrodesulfurization methods have the advantage of a high removal efficiency for thiophene compounds under mild conditions. However, independent nonhydrodesulfurization technologies are faced with their own shortcomings, such as limitations of the desulfurization performance and regeneration of materials. To overcome these limitations, four nanofluids were prepared by dispersing different metal-modified MCM-41 particles in deep eutectic solvent as multifunctional promoters to develop a comprehensive desulfurization method. Based on the excellent adsorbability and high catalytic activity of the dispersed particles and the outstanding extractability of deep eutectic solvent in nanofluids, a high sulfur removal of 99.33% was achieved for model oil under mild conditions in 15 min. The nanofluids also showed excellent reusability due to their high structural stability. In addition, NF@Cu/Al-MCM-41-2.5% exhibited the best desulfurization performance among the prepared nanofluids. This result was obtained because the introduction of Al ions increased the number of acid sites and defect sites to improve the catalytic activity and adsorbability, and the best affinity of Cu/Al-MCM-41 for the deep eutectic solvent favored the reaction mass transfer. This work opens the door to the development of a comprehensive nonhydrodesulfurization method based on the design of nanofluid materials.