Hydrogenation upgrading is an effective technique that lowers the oxygen content of bio-oil with the aim of improving its quality. In order to fabricate a series of Ru-based catalysts for the hydrodeoxygenation of bio-oil, several all-silica supports with different pore sizes are synthesized and modified with Al and Cs in this work. The physical morphology and electronic structure of the catalysts are characterized using multiple techniques including X-ray diffraction, in-situ pyridine adsorption infrared spectroscopy, in-situ diffuse reflectance Fourier transform infrared spectroscopy, Raman spectroscopy, CO2 temperature-programmed desorption, scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, X-ray photoelectron spectroscopy and N2 physical adsorption-desorption testing. Phenol, guaiacol, anisole and o-cresol are selected as model compounds to investigate the hydrodeoxygenation reactivity of the catalysts. The results reveal that there is a strong linear correlation between the pore size of the catalysts and the rates of the hydrogenation and hydrodeoxygenation of phenol. Importantly, both the oxygen vacancy density and relative content of Brønsted and Lewis sites (B/L) of the catalysts can be greatly increased by Cs modification, which further linearly promotes the hydrodeoxygenation activity of the catalysts. In addition, the in-situ infrared spectroscopy results show that the catalysts modified by Al and Cs heterolytically cleave H2 to supply H+ for the reaction. This work presents a novel approach for fabricating catalysts employed in the hydrotreatment process of bio-oil.