Metal nanoparticle-organic interfaces are common but remain elusive for controlling reactions due to the complex interactions of randomly formed ligand-layers. This paper presents an approach for enhancing the selectivity of catalytic reactions by constructing a skin-like few-nanometre ultrathin crystalline porous covalent organic overlayer on a plasmonic nanoparticle surface. This organic overlayer features a highly ordered layout of pore openings that facilitates molecule entry without any surface poisoning effects and simultaneously endows favourable electronic effects to control molecular adsorption–desorption. Conformal organic overlayers are synthesised through the plasmonic oxidative activation and intermolecular covalent crosslinking of molecular units. We develop a light-operated multicomponent interfaced plasmonic catalytic platform comprising Pd-modified gold nanoparticles inside hollow silica to achieve the highly efficient and selective semihydrogenation of alkynes. This approach demonstrates a way to control molecular adsorption behaviours on metal surfaces, breaking the linear scaling relationship and simultaneously enhancing activity and selectivity.