The rational regulation of catalyst active sites at atomic scale is a key approach to unveil the relationship between structure and catalytic performance. Herein, we reported a strategy for the controllable deposition of Bi on Pd nanocubes (Pd NCs) in the priority order from corners to edges and then to facets (Pd NCs@Bi). The spherical aberration-corrected scanning transmission electron microscopy (ac-STEM) results indicated that Bi2O3 with an amorphous structure covers the specific sites of Pd NCs. When only the corners and edges of the Pd NCs were covered, the supported Pd NCs@Bi catalyst exhibited an optimal trade-off between high conversion and selectivity in the hydrogenation of acetylene to ethylene under ethylene-rich conditions (99.7% C2H2 conversion and 94.3% C2H4 selectivity at 170 °C) with remarkable long-term stability. According to the H2-TPR and C2H4-TPD measurements, the moderate hydrogen dissociation and the weak ethylene adsorption are responsible for this excellent catalytic performance. Following these results, the selectively Bi-deposited Pd nanoparticle catalysts showed incredible acetylene hydrogenation performance, which provides a feasible perspective to design and develop highly selective hydrogenation catalysts for industrial applications.