Desulfurization in fuel has become more and more important due to increasingly stringent environmental protection policies. Mesoporous materials have attracted considerable attention owing to their excellent abilities in various catalytic reactions. Herein, we report the synthesis of molybdenum-containing dendritic mesoporous silica spheres via a facile Stöber approach and employ them in the removal of organic sulfur compounds. The dendritic mesoporous silica spheres not only provide a large specific surface area and pore volume but also possess a high dispersion of molybdenum species. Under optimal conditions, sulfur removal of the refractory aromatic sulfur compound 4,6-DMDBT can reach 100% in 40 minutes with a low dosage of oxidant. The catalysts can be reused nine times without a significant decrease. Furthermore, an oxidative desulfurization process was proposed through gas chromatography-mass spectrometry (GC-MS) analysis.