This work delineates the first example for controlling product selectivity in metal-catalyzed hydrogenation of biomass by zeolite crystals. The key to this success is to combine the advantages of both Pd nanoparticles (highly active sites) and zeolite micropores (controllable diffusion of reactants and products), which was achieved from encapsulation of the Pd nanoparticles inside of silicalite-I zeolite crystals as a core shell structure (Pd@S-1). In the hydrogenation of biomass-derived furfural, the furan selectivity over the Pd@S-1 is as high as 98.7%, outperforming the furan selectivity (5.6%) over conventional Pd nanoparticles impregnated with S-1 zeolite crystals (Pd/S-1). The extraordinary furan selectivity in the hydrogenation over the Pd@S-1 is reasonably attributed to the distinguishable mass transfer of the hydrogenated products in the zeolite micropores.