Accurately manipulating the electronic structure of metal active sites under working conditions is central to developing efficient and stable electrocatalysts in industrial water-alkali electrolyzers. However, the lack of an intuitive means to capture the evolution of metal sites during the reaction state inhibits the manipulation of its electronic structure. Here, atomically dispersed Ru single-sites on cobalt nanoparticles confined onto macro-microporous frameworks (M-Co NPs@Ru SAs/NC) with tunable electron coupling effect for efficient catalysis of alkaline hydrogen evolution reaction (HER) are constructed. Using operando X-ray absorption and infrared spectroscopies, a dynamic CoRu bond shrinkage with strong electron coupling effect under working conditions is identified, which significantly promotes the adsorption of water molecules and then accelerates its dissociation to form the key H* over Ru sites for high HER activity. The well-designed M-Co NPs@Ru SAs/NC delivers efficient HER performance with a small overpotential of 34 mV at 10 mA cm−2 and a high turnover frequency of ≈4284 H2 h−1 at −0.05 V, 40 times higher than that of the benchmark Pt/C. This work provides a new point of view to manipulate the electronic structure of the metal active sites for highly effective electrocatalysis processes.