Ru/CeO2 catalysts with different amounts of surface oxygen vacancies were prepared by changing the morphology of CeO2. The conversion of Ce4+ to Ce3+ and the formation of Ru–O–Ce bonds led to enhancement of the amount of oxygen vacancies. Ru species of low crystallinity enriched with Ru4+ ions exist on the surface of CeO2 nanorods, while metallic Ru particles exist on CeO2 nanocubes. The low crystallinity of Ru species and high concentration of oxygen vacancies enhanced the adsorption of hydrogen and nitrogen and also led to desorption of surface hydrogen in the form of H2. Therefore, Ru/CeO2 nanorods showed high ammonia synthesis activities. On the contrary, lower catalytic activity was observed over Ru/CeO2 nanocubes catalyst because H2 and N2 adsorption was less favorable plausibly due to the large particle size of Ru species and low concentration of oxygen vacancies, and most of the hydrogen species were consumed in H2O formation.