Subsurface atomic configurations exert a profound influence on the surface electronic structures, thereby playing a critical role in electrocatalysis. However, an in-depth understanding of intricate three-dimensional surface/subsurface structures in catalysts remain limited due to the weak interfacial signal and the inherent complexity in local structural and compositional nuances. Here, by determining the entirety of surface and subsurface atomic structures in Pd@Pt model catalysts through atomic-resolution electron tomography, our investigation reveals the pivotal role of atomic-scale local chemical heterogeneity, driven by atomic interfacial diffusion at the core-shell interface, in modulating the electronic structures and consequently tuning the catalytic behaviors in electrocatalytic ethanol oxidation reaction. Density functional theory calculations further elucidate that the atomically interfacial diffusion notably enhances OH adsorption energy at Pt sites while decreases CO adsorption energy at Pd sites on the surface by shifting the d-band center. These results broaden the existing paradigm of atomic interplay between surface and subsurface realms in bimetallic catalysts at fundamental level, offering valuable information for efficient catalyst design.