The bifunctional catalysts containing metal nanoparticles and acidic centers have been widely used in the upgrading of biomass-derived molecules via a catalytic hydrodeoxygenation process, but the synergistic efficiency of metal acid is generally unsatisfactory. Herein, we report a core-shell catalyst containing aluminosilicate zeolite crystals encapsulated by alumina supported Pd nanoparticles (zeolite@Pd/Al2O3) to be highly efficient for the hydrodeoxygenation of biomass-derived molecules. Compared with the reference catalysts involving a physical mixture of zeolite crystals and Pd/Al2O3 (zeolite + Pd/Al2O3), Pd nanoparticles supported on the zeolite crystals (Pd/zeolite), and Pd nanoparticles fixed within zeolite crystals (Pd@zeolite), the zeolite@Pd/Al2O3 exhibits simultaneously high activity, alkane selectivity, and good recyclability in the continuous recycle tests. The advantages of the zeolite@Pd/Al2O3 catalyst are reasonably attributed to its maximized metal acid synergistic efficiency. Also, the enhanced synergistic effect hinders the coke formation in the hydrodeoxygenation process, leading to unchanged catalytic performances in the continuous recycle tests.