High selective hydrogenation and hydrodeoxygenation of biomass-derived compounds are still challenging especially under mild reaction conditions using heterogeneous catalysis. Here, we reported a one-step synthesis method that successfully prepared Pd species immobilized on NH2-MIL-125 (Ti) MOF frameworks which were named [email protected] and used as a highly efficient hydrodeoxygenation catalyst for the reduction of vanillin to 2-methoxy-4-methyl phenol in excellent yield with an atm of H2 pressure at room temperature. Pd(PPh3)4 was dispersed in a solvent containing the MOF precursors. Among them, the PPh3 ligand could be oxidized to remove and Pd particles in situ doped in MOF framework during the solvothermal process. Compare to immersed-Pd/MOF and Pd-MOF, [email protected] has higher catalytic efficiency because the smaller Pd particles encapsulated in MOF inhibit Pd over oxidation. Moreover, the different reduction products could be obtained selectively by tuning reaction time, and the catalyst realized to catalyze the highly effective transformation of a variety of biomass-derived compounds.