In the view of practical applications, synthesizing green and recyclable nanocatalysts under mild conditions were always been desired by scientists and industries. In this study, in order to obtain the clean gasoline, a novel nanocomposite (PMo12O40@MnFe2O40) based on polyoxometalate and ceramic was synthesized successfully with Aloe vera leaf extract by sol–gel method in extremely mild conditions. PMo12O40@MnFe2O40 is proposed as a green new recyclable and economic nanocatalyst for deep catalytic oxidative desulfurization (CODS) of real and model fuel (DBT, Th, and BT). The characterizations were carried out by different analysis methods including Fourier transform infrared (FT‐IR), X‐ray diffraction (XRD), scanning electron microscopy (SEM), and energy‐dispersive X‐ray spectroscopy (EDX), and the successful synthesis and immobilization were approved. After conducting the PMo12O40@MnFe2O4 in the CODS processes, optimum effective properties were investigated. The average efficiency of the nanocatalyst was found 98% for DBT and 96% for real fuel by optimum values of the properties (catalyst dosage, temperature, oxidation system, and different types of catalysts), not to mention its great ability in reusability with 96% of effectiveness after five runs. Moreover, the CODS mechanism is proposed, and based on the obtained results, the kinetics were in agreement with the pseudo‐first‐order model. Based on the obtained incomparable results, it could be considered as an effective, industrial‐scale, and green nanocatalyst for the desulfurization of refractory sulfur compounds in extremely mild conditions.