The electrocatalytic reduction of CO2 into value-added chemicals such as hydrocarbons has the potential for supplying fuel energy and reducing environmental hazards, while the accurate tuning of electrocatalysts at the ultimate single-atomic level remains extremely challenging. In this work, we demonstrate an atomic design of multiple oxygen vacancy-bound, single-atomic Cu-substituted CeO2 to optimize the CO2 electrocatalytic reduction to CH4. We carried out theoretical calculations to predict that the single-atomic Cu substitution in CeO2(110) surface can stably enrich up to three oxygen vacancies around each Cu site, yielding a highly effective catalytic center for CO2 adsorption and activation. This theoretical prediction is consistent with our controlled synthesis of the Cu-doped, mesoporous CeO2 nanorods. Structural characterizations indicate that the low concentration (<5%) Cu species in CeO2 nanorods are highly dispersed at single-atomic level with an unconventionally low coordination number ∼5, suggesting the direct association of 3 oxygen vacancies with each Cu ion on surfaces. This multiple oxygen vacancy-bound, single atomic Cu-substituted CeO2 enables an excellent electrocatalytic selectivity in reducing CO2 to methane with a faradaic efficiency as high as 58%, suggesting strong capabilities of rational design of electrocatalyst active centers for boosting activity and selectivity.