We investigated the microstructures of Au-deposited PtCo@Pt core-shell nanoparticles (NPs) and discussed enhancement of the oxygen reduction reaction (ORR) properties by Au termination of low-coordination sites of the Pt-shell. The Au-deposited PtCo@Pt NPs showed an improved electrochemical structural stability, together with slight increment in increased initial, pristine area-specific activity relative to the non-Au-deposited PtCo@Pt NPs. Atomic-level microstructural characterization was performed by a back-side illumination fluorescence X-ray absorption fine structure (BI-FXAFS) method and scanning transmission electron microscopy with energy dispersive spectroscopy (STEM-EDS). The BI-FXAFS results indicated that compressive lattice strain in the Pt-shells of the PtCo@Pt NPs was almost unchanged by the subsequent Au deposition. Furthermore, STEM-EDS mapping of Pt, Co, and Au clearly showed that the deposited Au tended to localize at low-coordination sites of the Pt-shell surface, e.g., edges and corners. The atomic-level microstructural characterization conducted in this study demonstrated that effective Au surface terminations of the Pt-shell enhance the ORR durability of Pt-based core-shell type NP catalysts.