Zeolite catalysts have been widely applied in petroleum and chemical industries. Nano/hierarchical structure could improve the utilization efficiency of active sites, especially for metal species encapsulated in zeolites. However, the uniformity of zeolite surface and crystallinity would decrease, leading to low stabilization effect. Herein, we developed a seed-directed method to prepare Pd clusters (∼1.3 nm) regioselectively encapsulated in hollow polycrystalline shell of Silicalite-1 zeolite. In nitrobenzene hydrogenation reaction, the optimized Pd@S-1-hp showed a high conversion of 92.2% at 110°C, which is 40% higher than that of Pd clusters in bulk zeolite. Sub-nano Pd species in polycrystalline shell could significantly shorten the diffusion length on the basis of strong microporous confinement effect. Catalytic hydrogenation activity remained stable after six cycles. This structure could be extended to heterogeneous reactions suffering from diffusion limitation.