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 CeO₂ spheres (Ir₁@CeO₂). When applied to the hydrogenation of α,β-unsaturated aldehydes, Ir₁@CeO₂ catalyst remarkably exhibited ~ 100% selectivity towards unsaturated alcohols, whereas the formation of Ir nanoparticles on CeO₂ drastically decreased the selectivity for unsaturated alcohols. Spectroscopic studies revealed that strong metal–support interactions triggered the charge transfer from Ir to CeO₂, leading to the partial reduction of Ce⁴⁺ to Ce³⁺ along with the formation new Ir^δ+–O^2––Ce³⁺(O_V) interfaces. The electrophilic atomic Ir species at the Ir^δ+–O^2––Ce³⁺ (O_V) interfaces would therefore preferentially adsorb and facilitate hydrogenation of polar C=O bond to achieve exceptional selectivity.