Heterogeneous catalytic oxidation, Fenton-like (FL) hybrid nanoparticles (NPs) induced by microwave (MW) irradiation, was applied as a green technology pathway for methomyl pesticide oxidation. Three different hybrid nanostructured particles, C300, C400 and C500 containing various phase structures, i.e., Cu, Cu2O and CuO, were successfully synthesized by the thermal decomposition technique and used as a FL source in microwave-induced (MW/FL) system. The microstructure and morphology of the hybrid nanostructured particles were studied using an X-ray diffraction (XRD) field-emission scanning electron microscope (FE-SEM), respectively. Also, MW/FL system was compared to MW/H2O2 and (MW) alone. The influence of various operating parameters, i.e., microwave irradiation time and power, initial NPs concentration, H2O2 concentration and pH for the three MW/FL systems, was investigated, and the optimal operating conditions were compared. The results indicated that the MW/FL process outperformed the other systems, and around 91% of methomyl was removed after only 8 min of MW irradiation for the C300-based MW/FL system under optimal conditions. Notably, the results verified that the heterogeneous MW/FL oxidation system catalyzed over the synthesized NPs reacted with the wastewater at its initial pH without adjustment, which overcomes the weakness of the homogeneous Fenton catalyst. Hence, this advantage could expand the application of this oxidation technique and thus improves the system efficiency. Finally, the catalyst showed good reusability. The success of this technique explores the possibility of copper as a non-iron FL system in a MW-assisted system for the rapid removal of methomyl from wastewater.