Hydrodeoxygenation (HDO) of bio-oils obtained by rapid pyrolysis of biomass into high value-added chemicals generally required harsh conditions. Herein, three kinds of mixed-phase ZrO2 supports (denoted as ZSX, X = 2–4) with different crystal structure proportions were prepared by one-pot hydrothermal synthesis method, and their performance on the properties of Pd/ZrO2 catalysts were investigated for vanillin HDO. Pd/ZS3 exhibited excellent efficiency in HDO of vanillin, a typical model compound of lignin, achieving approximately 100% yield of 2-methoxy-4-methylphenol (MMP) in presence of n-butanol as solvent and polymethyl hydrogen siloxane (PMHS) as hydrogen donor under mild conditions (35 °C, 1 h). It was due to catalytic synergy of exposed metal active sites, oxygen vacancies (Ov) and acid sites to occur electron transfer and enhance interaction between Pd and ZrO2. By tuning the crystal structure of ZrO2 support, the influence of Ov and acid sites of Pd/ZrO2 over vanillin HDO performance was investigated, Pd/ZS2 with abundant Ov and Pd/ZS4 with substantial acid sites promoted hydrogenation and hydrogenolysis, respectively, Pd/ZS3 possessed preferable conversion and selectivity as having the properties of both at once. Additionally, reaction pathway was also proposed in which vanillin was converted to MMP by combining intermediate of 4-hydroxy-methyl-2-methoxyphenol (HMP) with active hydrogen species while removing water. This developed catalysts with different crystalline highlighted an enormous promise for HDO of bio-oils into green fuel under mild conditions.