Three-dimensional (3D) atomic arrangements in the surface and subsurface parts of nanomaterials are crucial for understanding their structure-functionality correlations. However, unveiling the required structure at such a resolution remains a challenge due to the lack of effective imaging and reconstruction techniques. Here, we determine the 3D atomic surface and subsurface structures of Au@Pd core-shell nanoparticles and study their correlations with electronic and surface chemical properties using atomic-resolution electron tomography (AET). We find that the intermixing of Au and Pd is the key factor that influences the surface and subsurface structure and quantitatively reveals its negative correlations with bond disorder and tensile strain. By applying spectroscopic and electrochemical measurements, we confirm that different surface structures modify the electronic and chemical properties at different Au/Pd ratios. These results not only shed light on the complex surface and subsurface structures of realistic nanomaterials but also deepen our understanding of structure-functionality correlations in nanostructures at the single-atom level.