<p>Subsurface regions critically govern surface events, such as the interactions with reactants in heterogeneous catalysis, thereby significantly modulating catalytic performance. However, precise control of subsurface atomic arrangement remains challenging due to complex metal-adsorbate interactions and limited structural accessibility. Here we achieve precise control of subsurface atomic layer in platinum-based intermetallic compounds through targeted positioning of heterometallic atoms to subsurface via in-situ constructed atomic diffusion pathways. This site-specific placement and subsequent thermodynamic-induced atomic rearrangement are governed by surface energy minimization and adsorbate-induced segregation. Through atomic-precision subsurface engineering, we successfully synthesize a series of L1₀ (face-centered tetragonal, fct)-PtFe@PtM_sub, where M_sub represents heteroatoms (Ru, Rh, Pd, Ag) incorporated into subsurface layers. As demonstrated, the as-synthesized L1₀-PtFe@PtPd_sub simultaneously stabilizes ligand and strain effects, thereby breaking the trade-off in L1₀-PtM with Pt skin, where Pt skin typically quenches ligand effects while introducing strain effects. Consequently, L1₀-PtFe@PtPd_sub/C catalyst demonstrates practical proton exchange membrane fuel cells performance, simultaneously delivering high activity and durability. This work provides a rational strategy for catalyst design that promotes the understanding of subsurface active sites in heterogeneous catalysis.</p>