We report here a strategy for the facile synthesis of hierarchical MFI zeolite nanocrystals with controllable inter-crystalline mesopores by a one-step hydrothermal synthesis method using silica gel as the silica source and tetrapropyl ammonium as the microporous template without any other mesoporous templates or zeolite seeds. Powder X-ray diffraction results show the MFI structure with high crystallinity for all as-prepared zeolites. Scanning electron microscope characterization shows that 400–1000 nm zeolite aggregates are composed of the assembly of ~100 nm zeolite nanocrystals. Transmission electron microscopy results indicate the formation of inter-crystalline mesopores in the aggregated nanocrystals among the interspace of zeolite nanocrystals. The high mesopore volume (0.13 cm³ g⁻¹) and external surface area (93 cm² g⁻¹) of the aggregated MFI zeolites are observed by N₂ sorption measurements. The inter-crystalline porosity of MFI zeolites varies with the change in aggregation and the size of zeolite nanocrystals by changing the sodium concentration or the type of sodium salt in aluminate–silicate gels during hydrothermal crystallization. The mesoporous MFI zeolite aggregates exhibit similar light olefin selectivities and remarkably enhanced lifetime in the catalytic cracking of hexane compared to the highly dispersed MFI zeolite nanocrystals.