Hydrodeoxygenation (HDO) reactions are extensively employed in the conversion of biomass to advanced fuels, which rely heavily on bifunctional catalysts that contain both a metal component and an acidic component. A significant challenge in the development of HDO catalysts is the need to reduce costs while simultaneously enhancing catalytic efficiency. Here, a series of Ru@W/ZrO2 catalysts with an extremely low loading of Ru (0.5 wt%) were successfully synthesized using different Ru or W loading sequences and different Ru/W mass ratios. The catalysts were applied in the HDO reaction of lignin-derived phenols, and their physical and chemical characteristics were revealed by various characterization techniques, including XRD, H2-TPD, NH3-TPD, and XPS. The results suggest that the synthesis method with post-loading Ru leads to improved exposure and utilization of the low-loaded Ru, which effectively serves as the active sites for hydrogenation in catalytic reactions. Under the same reaction conditions, the bifunctional catalyst with post-loading of Ru achieved a complete conversion of phenol into cyclohexane, while the catalyst with simultaneous loading of Ru and W only yielded 42% of cyclohexane. In addition, the Ru/W ratios have also shown significant effects on the HDO performance of the catalyst. The catalyst exhibits the highest hydrogenation activity when the Ru/W ratio is 10, which is further supported by kinetic experiments. This study highlights the significance of the loading sequence of noble metals and the metal/acid ratio in the synthesis of highly active bifunctional catalysts, and also lays the groundwork for the efficient utilization of noble metals in biomass HDO conversion.