Hydrogen production from electrochemical water splitting is a promising route to pursue clean and sustainable energy sources. Here, a three-dimensional nanoporous Cu–Ru alloy is prepared as a high-performance platinum-free catalyst for hydrogen evolution reaction (HER) by a dealloying process. Significantly, the optimized nanoporous alloy Cu53Ru47 exhibits remarkable catalytic activity for HER with nearly zero onset overpotential and ultralow Tafel slopes (∼30 and ∼35 mV dec–1) in both alkaline and neutral electrolytes, achieving a catalytic current density of 10 mA cm–2 at low overpotentials of ∼15 and ∼41 mV, respectively. Operando X-ray absorption spectroscopy experiments, in conjunction with DFT simulations, reveal that the incorporation of Ru atoms into the Cu matrix not only accelerates the reaction step rates of water adsorption and activation but also optimizes the hydrogen bonding energy on Cu and Ru active sites, improving the intrinsic activity for HER.