Abstract Pd nanoparticles were successfully encapsulated inside mesoporous silicalite‐1 nanocrystals (Pd@mnc‐S1) by a one‐pot method. The as‐synthesized Pd@mnc‐S1 with excellent stability functioned as an active and reusable heterogeneous catalyst. The unique porosity and nanostructure of silicalite‐1 crystals endowed the Pd@mnc‐S1 material general shape‐selectivity for various catalytic reactions, including selective hydrogenation, oxidation, and carbon–carbon coupling reactions.