Atomic dispersed metal sites in single‐atom catalysts are highly mobile and easily sintered to form large particles, which deteriorates the catalytic performance severely. Moreover, lack of criterion concerning the role of the metal–support interface prevents more efficient and wide application. Here, a general strategy is reported to synthesize stable single atom catalysts by crafting on a variety of cobalt‐based nanoarrays with precisely controlled architectures and compositions. The highly uniform, well‐aligned, and densely packed nanoarrays provide abundant oxygen vacancies (17.48%) for trapping Pd single atoms and lead to the creation of 3D configured catalysts, which exhibit very competitive activity toward low temperature CO oxidation (100% conversion at 90 °C) and prominent long‐term stability (continuous conversion at 60 °C for 118 h). Theoretical calculations show that O vacancies at high‐index {112} facet of CoxOy nanocrystallite are preferential sites for trapping single atoms, which guarantee strong interface adhesion of Pd species to cobalt‐based support and play a pivotal role in preventing the decrement of activity, even under moisture‐rich conditions (≈2% water vapor). The progress presents a promising opportunity for tailoring catalytic properties consistent with the specific demand on target process, beyond a facile design with a tunable metal–support interface. Single‐atom catalysts are achieved on tunable cobalt‐based nanoarrays through crystal facet induced atom trapping. By precisely controlling the metal–support interface, favorable surface chemistry can be provided to create configured heterogeneous Pd/CoxOy catalysts, which exhibit superior activity for low‐temperature oxidation (100% CO conversion at 90 °C) and prominent long‐term stability.