A novel N‐doped MoO3@SiC hollow nanosphere has been synthesized through two steps. Due to the first step, N‐doped MoO2@C nanosphere was synthesized using the hydrothermal method and in the second step, Si‐C bonds were formed through the low‐temperature magnesiothermic method and MoO3@SiC hollow nanosphere was produced. The prepared nanostructures were identified by various techniques such as IR, XRD, XPS, BET/BJH, SEM/EDS, and Raman spectroscopy. Results show that converting of C to SiC increase the surface area from 17 to 241 m2/g with remarkably decrease in pore diameter. Also, molybdenum is present in the form of MoO2 in carbon catalyst while during magnesiothermic process, it transfers to MoO3 form in the SiC catalyst. The synthesized products were employed as catalysts in oxidative desulfurization of model fuel. The results displayed that MoO3@SiC hollow nanostructure shows a superior catalytic activity (99.9%, 40 min) compared to C support (56%, 60 min). Furthermore, the recycling of MoO2@C catalyst shows a dramatic decrease even after the first run, while, SiC support exhibit higher stability during the stronger interaction between molybdenum catalyst and SiC support.