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Efficient and sustainable energy conversion depends on the rational design of single-atom catalysts. The control of the active sites at the atomic level is vital for electrocatalytic materials in alkaline and acidic electrolytes. Moreover, fabrication of effective catalysts with a well-defined surface structure results in an in-depth understanding of the catalytic mechanism. Herein, a single atom ruthenium dispersed in nickel-cobalt layered hydroxide (Ru-NiCo LDH) is reported. Through the precise controlling of the atomic dispersion and local coordination environment, Ru-NiCo LDH//Ru-NiCo LDH provides an ultra-low overpotential of 1.45 mV at 10 mA cm−2 for the overall water splitting, which surpasses that of the state-of-the-art Pt/C/RuO2 redox couple. Density functional theory calculations show that Ru-NiCo LDH optimizes hydrogen evolution intermediate adsorption energies and promotes O-O coupling at a Ru-O active site for oxygen evolution, while Ni serves as the water dissociation site for effective water splitting. As a potential model, Ru-NiCo LDH shows enhanced water splitting performance with potential for the development of promising water-alkaline catalysts.