Silica is one of the most referenced materials for the preparation of heterogeneous metal catalysts. However, silica spheres with smooth surfaces have difficulty encapsulating active metals due to their small surface area and the presence of only a handful of silicon hydroxyl groups on the surface. In this work, the silica sphere has been first consciously transformed into a hierarchical SiO2@silicate structure, and then the core–shell hetero-structured SiO2@Ni/SiO2 catalyst can be tactfully obtained by reducing treatment. The core–shell catalyst is composed of a rigid core (SiO2) and a rough shell (Ni NPs highly disperse on nanosheet SiO2), which are carefully verified by X-ray diffraction (XRD), transmission electron microscope (TEM), field scanning electron microscope (FESEM), H2-TPR/TPD and X-ray photoelectron spectroscopy (XPS). The derived SiO2@Ni/SiO2 catalyst can selectively hydrogenate vanillin in the aqueous phase at near-room temperature (40 ℃) and low hydrogen pressure (2 MPa H2), and the conversion of vanillin can be up to 99%. The preparation method of the SiO2@Ni/SiO2 catalyst is simple and can be amplified to a large scale at a low price, thus can be adopted to convert bio-derived unsaturated compounds in an economical and eco-friendly way.