In this manuscript, an organic-inorganic hybrid nanocatalyst has been synthesized using an ionic liquid as a transfer agent, copper oxide nanoparticles as a support, and the highly active mono copper-substituted polyoxotungstate. Ultrasound-assisted extractive-catalytic oxidative desulfurization (UA-ECODS) method was proposed to remove the Benzothiophene (BT), Dibenzothiophene (DBT), and 4,6-Dimethyl dibenzithiophene (4,6-DMDBT) in diesel fuel and straight run gas oil. The process involves the simultaneous use of extraction technique by an ionic liquid ([BMIM][PF6]) and catalytic oxidation by a suitable heterogeneous catalyst. The experimental condition was optimized by response surface methodology. The removal efficiency in the three compounds was as follows: BT < DBT < 4,6-DMDBT. In addition, the kinetic behavior of the removal of all three sulfur compounds was according to a quasi-first-order model. The reaction rate constant and apparent activation energy was calculated at 5 different temperatures.