Nanostructure control is an important improvement strategy for zeolite catalyst. A novel hierarchical core/shell zeolite structure with mesoporous core and thin microporous Silicalite-1 shell was prepared by secondary coating of mesoporous ZSM-5 in this paper. The zeolite structure was proved by the combination of broad characterization techniques especially electron microscopy from different length scales. The combination of focused ion beam scanning electron microscope (FIB-SEM) and scanning transmission electron microscopy (STEM) clearly proved the formation of desired core/shell structure. The as-prepared core-shell structured hierarchical MFI (Framework Type) zeolite showed a high hydrothermal stability, unique acidic property and outstanding catalytic performance in methanol to hydrocarbon reaction and biomass catalytic pyrolysis. The synthesis strategy could be extended to other zeolites and generated a family of novel hierarchical zeolites.