Novel and highly stable nitronyl nitroxide radical (NIT) derivatives were synthesized and coated on the surface of multi-walled carbon nanotubes (MWCNTs) to improve their desulfurization performance. They were characterized by FTIR, UV-vis, SEM, XRD, Raman spectroscopy and ESR. Thiophene in fuel was desulfurized by molecular O2, and the oxidation activity of these compounds was evaluated. At a normal temperature and pressure, the degradation rates of thiophene by four compounds in 4 h can reach 92.66%, 96.38%, 93.25% and 89.49%, respectively. The MWCNTs/NIT-F have a high special activity for the degradation of thiophene, and their desulfurization activity can be recycled for five times without a significant reduction. The mechanistic studies of MWCNTs/NIT composites show that the ammonium oxide ion is the key active intermediate in catalytic oxidative desulfurization, which provides a new choice for fuel oxidative desulfurization. The results show that NIT significantly improves the photocatalytic performance of MWCNTs.