Metal-zeolite catalysts are promising for hydrodeoxygenation of bio-oils, but they always encounter sluggish diffusion kinetics due to sole micropores and inferior metal stability. Here, highly stable sub-nanoscale Pt-Ni bimetals confined in a hierarchical ZSM-5 zeolite (Pt-Ni@HZ) are constructed. The formed Pt-Ni@HZ species create framework-bonding metal sites with zeolite in a confined microenvironment, thereby establishing strong interactions and generating uniform distribution of Pt-Ni bimetals. In the Pt-Ni@HZ-catalyzed hydrodeoxygenation of phenolics, sub-nanometric Pt-Ni facilitates the adsorption and transfer of hydrogen, and hierarchical pores promote the diffusion kinetics of reactants. The designed Pt-Ni@HZ with small metal particles and high coordination numbers of Pt-Ni bonds, favors the complete deoxygenation of phenolics, with a higher yield of cyclohexane than conventional catalysts prepared by impregnation. Benefiting from the protection of the zeolite framework, the Pt-Ni@HZ catalyst exhibits high thermal stability and low leaching of metal active sites, with only 4.4 % catalyst deactivation after five reaction cycles.