Selective hydrogenation of the carbonyl bond in α,β-unsaturated carbonyl compounds is rather challenging owing to the more feasible hydrogenation of ethylenic bond from both thermodynamic and kinetic aspects. Here, we demonstrate a facile emulsion-based molecule-nanoparticle self-assembly strategy for the atomic engineering of Ir species on three-dimensional CeO spheres (Ir@CeO). When applied to the hydrogenation of α,β-unsaturated aldehydes, Ir@CeO catalyst remarkably exhibited ~ 100% selectivity towards unsaturated alcohols, whereas the formation of Ir nanoparticles on CeO drastically decreased the selectivity for unsaturated alcohols. Spectroscopic studies revealed that strong metal—support interactions triggered the charge transfer from Ir to CeO, leading to the partial reduction of Ce to Ce along with the formation new Ir—O—Ce(O) interfaces. The electrophilic atomic Ir species at the Ir—O—Ce (O) interfaces would therefore preferentially adsorb and facilitate hydrogenation of polar C=O bond to achieve exceptional selectivity. [Figure not available: see fulltext.].