A one-step method to synthesize small size cup-like hollow ZSM-5 single crystals is reported in this paper. Characterization methods show that the product has a typical ZSM-5 structure and most crystals are uniform, mono dispersed crystal shells with distinct hollow structure. The average size of a single crystal is about 350 nm. Every cup-like hollow ZSM-5 crystal can act as a microreactor in the reaction, and the ZSM-5 based catalyst POM-MOF-ZSM-5 (polyoxometalates (POM), metal–organic frameworks (MOF)) shows excellent oxidative desulfurization performance of DBT (dibenzothiophene).