The practical application of non-noble metal-based hydrogenation catalysts is limited because of their low activity and easy oxidation in air. Here, porous silica-supported ultrafine nickel oxide (NiO) was prepared by calcining an organic–inorganic hybrid 3D nanomaterial that was formed via the Michael addition/Schiff’s base reaction, and hydrolyzation of triethoxysilane. NiO nanoparticles with ca. 2.6 nm diameter was uniformly dispersed and confined in the cogenerated mesoporous SiO2 skeleton, thanks to the coordination between pyrogallol/amino units and Ni2+ ions, and the isolation effect of Si-O-Si network. The as-prepared catalyst featured mesoporous structure and high specific surface area (715 m2/g), and exhibited excellent activity, selectivity and reusability in the semi-hydrogenation of alkynes. Small amount of metallic nickel (Nix-NiO) that formed on the surface of NiO nanoparticles during the semi-hydrogenation acted as the active species, and the moderate adsorption/desorption energies on Nix-NiO facilitated the activity enhancement. Most importantly, it showed constant catalytic activity and selectivity after a long-term storage in air. This work provides a green and feasible strategy, as an alternative to the traditional impregnation method, for the preparation of ultrafine metal-supported catalysts with air-stability and reusability.