CO2 methanation might be an efficient way to reduce the greenhouse effect and solve the energy problems. The supported Ru catalysts are one of the most widely used methanation catalysts, but the effect of the Ru particles' micro-morphology on the CO2 methanation was rarely studied theoretically. The Run/Ru(0001) (n = 1, 2, 3, 4) was built for modeling the defected Ru sites with low Ru-Ru coordination numbers (CN = 3, 4, 5, and 5.5) in the present work. On the Run/Ru(0001) (n = 1, 2, 3, 4), the most favored pathway for CH4 formation is the COH route: CO2 → CO → COH → C → CH → CH2 → CH3 → CH4. Based on the microkinetic modeling results, we find the selectivity for CH4 increases when the CN of Ru increases from 3 to 5.5, and the selectivity is almost 100% over Ru4/Ru(0001). However, the selectivity for CO is the opposite, that is, the Ru ensemble with lower CN is favorable for CO formation. This study reveals the strong relationship between the Ru-Ru CN and the CO2 methanation reactivity/selectivity and finds the model catalysts with about fiver Ru-Ru CN exhibit the best methanation property. Consequently, metal nanoparticles with more fractions of five-coordinated Ru-Ru configurations would be beneficial for CO2 methanation.