Hydrogen evolution reaction (HER) is a critical process due to its fundamental role in electrocatalysis. Practically, the development of high-performance electrocatalysts for HER in alkaline media is of great importance for the conversion of renewable energy to hydrogen fuel via photoelectrochemical water splitting. However, both mechanistic exploration and materials development for HER under alkaline conditions are very limited. Precious Pt metal, which still serves as the state-of-the-art catalyst for HER, is unable to guarantee a sustainable hydrogen supply. Here we report an anomalously structured Ru catalyst that shows 2.5 times higher hydrogen generation rate than Pt and is among the most active HER electrocatalysts yet reported in alkaline solutions. The identification of new face-centered cubic crystallographic structure of Ru nanoparticles was investigated by high-resolution transmission electron microscopy imaging, and its formation mechanism was revealed by spectroscopic characterization and theoretical analysis. For the first time, it is found that the Ru nanocatalyst showed a pronounced effect of the crystal structure on the electrocatalytic activity tested under different conditions. The combination of electrochemical reaction rate measurements and density functional theory computation shows that the high activity of anomalous Ru catalyst in alkaline solution originates from its suitable adsorption energies to some key reaction intermediates and reaction kinetics in the HER process.