The development of highly active, reusable catalysts for aqueous-phase reactions is challenging. Herein, metallic nickel is encapsulated in a nitrogen-doped carbon–silica composite (SiO2@Ni@NC) as a catalyst for the selective hydrogenation of vanillin in aqueous media. The constructed catalyst achieved 99.8% vanillin conversion and 100% 4-hydroxymethyl-2-methoxyphenol selectivity at room temperature. Based on combined scanning transmission electron microscopy, X-ray photoelectron spectroscopy, and Raman analyses, the satisfactory catalytic performance is attributed to the composite structure consisting of an active metal, carbon, and silica. The hydrophilic silica core promoted dispersion of the catalyst in aqueous media. Moreover, the external hydrophobic NC layer has multiple functions, including preventing oxidation or leaching of the internal metal, acting as a reducing agent to reduce the internal metal, regulating the active-site microenvironment by enriching the concentrations of H2 and organic reactants, and modifying the electronic structure of the active metal via metal–support interactions. Density functional theory calculations indicated that NC facilitates vanillin adsorption and hydrogen dissociation to promote aqueous-phase hydrogenation. This study provides an efficient strategy for constructing encapsulated Ni-based amphiphilic catalysts to upgrade biomass-derived compounds.