The Haber-Bosch process for NH3 production is one of the largest global energy consumers. Despite improvements over the past century, developing catalysts with enhanced activities and durabilities remains challenging. Ru-based catalysts supported on CeO2 are suitable alternatives under mild reaction conditions. Here, we elucidated the effects of Ru structure on the physicochemical properties and catalytic activities of Ru-CeO2 systems. One-pot syntheses with metal–organic frameworks as sacrificial templates were used to prepare Ru single-atom, nanocluster, and nanoparticle systems. The Ru nanoclusters and single atoms exhibited superior and more stable performances toward NH3 production, with no hydrogen poisoning, in relation to the Ru nanoparticles. Kinetic data and electronic energy calculations demonstrated that the Ru nanoclusters coexisting with Ru single atoms may maximize the NH3 synthetic activity via the combination of dissociative and associative mechanisms. These results provide guidance for the rational design and optimization of Ru-based catalysts for use in NH3 synthesis.