5-Hydroxymethylfurfural (HMF) is a pivotal multifunctional platform compound. The transformation of glucose to HMF generally follows tandem catalysis including the isomerization of glucose to fructose and the dehydration of fructose to targeted product HMF. Designing robust catalyst with high diffusion performance is highly desired. Besides, the catalytically active site (Lewis or Brønsted acid) for the second step of fructose dehydration is still a pending question. Herein, Sn-containing Sn-Y zeolite with hierarchical channel systems was post-synthesized through successive acid dealumination and stannation treatment. Sn ions existed in a tetra-coordinated state in zeolite framework. Precisely controlling acid treated time was necessary to prepare robust Sn-Y zeolite catalyst in the conversion of glucose to HMF, which was closely related to Al and Sn contents. Structure-performance relationship revealed that the first step of glucose isomerization was triggered by Lewis acid site, while both Lewis and Brønsted acid sites can fuel the second step of fructose dehydration. Under the optimal reaction conditions, Sn-Y zeolite catalyst exhibited extraordinary catalytic performance, outperforming most of other reported zeolite catalysts. It is likely due to the excellent diffusion performance contributed by the opened pores and hierarchical channel systems. Finally, the reusability, deactivated mechanism, and regenerated method were also investigated in detail. The catalytic performance of deactivated catalyst can be easily restored to initial level through a simple calcination method.