For size-sensitive catalytic reaction systems, precise control of geometric size of heterogeneous transition metal catalysts, especially for non-noble metals, is in desperate need and also a great challenge. Here, highly dispersed Ni nanoparticles (NPs) anchored within mesoporous silica (MS) is fabricated through a hybrid strategy of amino-modification and vacuum-impregnation. The Ni NPs in Ni/MS catalyst can be precisely regulated from 2.2 to 12.6 nm, causing a variation in the proportion of low and high coordination sites of Ni atoms. The Ni/MS catalysts show a volcanic trend between 2-methoxy-4-methylphenol (MMP) yield and Ni geometry size in hydrodeoxygenation (HDO) of bio-derived vanillin, and the Ni/MS-4.8 catalyst with middle size (4.8 nm) shows optimal HDO performance with the highest MMP productivity of 19.5 gMMP gNi−1 h−1. DFT calculation demonstrates that the medium-sized Ni/MS-4.8 catalyst possesses abundant low/high coordinated Ni atoms, wherein the low coordinated Ni atoms facilitate the adsorption of H2 and vanillin, and the high coordinated Ni atoms promote the dissociation of H2 and activating of C═O and C─O bonds, thus displays superior performance in HDO reaction. This work paves a way in precise control of geometric size of heterogeneous catalysts applicating in size-sensitive catalysis.