The ability to finely tune the nuclearity of active metal sites is critical for designing highly selective catalysts, especially for hydrogenation processes. In this work, we developed a novel PdCu catalyst with an ordered body-centered cubic (BCC) structure, enabling precise control over Pd nuclearity to optimize selectivity. Using a facile polyol synthesis method, we modulated the Pd coordination environment, reducing the Pd-Pd coordination number from 3 (disordered face-centered cubic, FCC) to 0 (ordered BCC), thereby achieving full isolation of Pd by the surrounding Cu atoms. This structural transformation enhances hydrogen spillover and weakens ethylene adsorption, resulting in superior activity for the selective hydrogenation of acetylene to ethylene. The ordered PdCu supported on Al2O3 (o-PdCu/Al2O3) achieved a 99% acetylene conversion with an 84.5% ethylene selectivity at near-room temperature. This work highlights the importance of controlling atomic-scale nuclearity in metal catalysts and provides a promising strategy for improving the catalytic efficiency and selectivity in industrially significant processes.