Shifting from the typical 4e– pathway to H2O in electrochemical oxygen reduction to the 2e– pathway to H2O2 is increasingly recognized as an environmentally friendly approach for producing H2O2. However, the competitive 4e− pathway is a significant obstacle to the production of H2O2 since H2O is the thermodynamically favored product. Here, a series of Pt, Pd, and Rh active atoms diluted within inert‐Au matrices with precisely controlled atomic arrangements and coordination environments are synthesized via facet engineering for O2‐to‐H2O2 production. Surprisingly, individually dispersed Pt atoms within the Au surface enclosed by the square atomic arrangements exhibit superior H2O2 selectivity and achieve a maximum selectivity of 90% at 0.36 V versus the reversible hydrogen electrode. Operando synchrotron ambient pressure X‐ray photoelectron spectroscopy identifies the presence of *OOH key intermediates on these isolated Pt active sites. Grand canonical density‐functional theory also reveals that the kinetic energy barrier for the 2e− pathway (0.08 eV; OOH* + H+ + e− →  H2O2) on the isolated Pt sites is significantly lower than the 4e− pathway (0.29 eV; OOH* + H+ + e− → O* +  H2O). This work enables atomic‐scale control in dilute binary alloy surfaces with specific configurations of isolated active atoms and provides essential guidance for catalyst design to boost O2‐to‐H2O2 production. Active Pt, Pd, and Rh atoms dispersed in inert‐Au matrices with controlled atomic arrangements and coordination environments are synthesized for electrocatalytic O2‐to‐H2O2 production. Surprisingly, isolated Pt atoms enclosed by square arrangements exhibit superior H2O2 selectivity of 90%. Operando X‐ray photoelectron spectroscopy and density‐functional theory uncover *OOH intermediates, highlighting a lower kinetic barrier of 0.08 eV for two‐electron oxygen reduction reaction.