In this work, the highly active polyoxometalate (PW2Mo2) with Venturello structure and its corresponding catalyst were applied in catalytic desulfurization for the first time. PW2Mo2 as an active component was effectively encapsulated in hollow periodic mesoporous organosilica (HPMOS) to form the nanoreactor PW2Mo2@HPMOS, where the central cavity and mesoporous shell facilitate mass transfer and both provide a stable place to react with organic sulfides. Desulfurization test results show that the hollow nanoreactor PW2Mo2@HPMOS can almost remove four sulfides simultaneously from diesel in 2 h under mild conditions. Besides, the nanocatalyst PW2Mo2@HPMOS can be reused and recycled for at least seven consecutive tests without any noticeable loss in performance. With the rapid development of the economy, the massive use of sulfur-containing fuel has a huge impact on the global climate. After combustion of sulfur-containing fuel, the realized SOX is an important inducement of the formation of acid rain, and the realized sulfur particle is also a major source of haze. Therefore, removing sulfur compounds from fuel is an important issue that needs to be solved immediately.