Although metastable crystal structures have received much attention owing to their utilization in various fields, their phase‐transition to a thermodynamic structure has attracted comparably little interest. In the case of nanoscale crystals, such an exothermic phase‐transition releases high energy within a confined surface area and reconstructs surface atomic arrangement in a short time. Thus, this high‐energy nanosurface may create novel crystal structures when some elements are supplied. In this work, the creation of a ruthenium carbide (RuCX, X < 1) phase on the surface of the Ru nanocrystal is discovered during phase‐transition from cubic‐close‐packed to hexagonal‐close‐packed structure. When the electrocatalytic hydrogen evolution reaction (HER) is tested in alkaline media, the RuCX exhibits a much lower overpotential and good stability relative to the counterpart Ru‐based catalysts and the state‐of‐the‐art Pt/C catalyst. Density functional theory calculations predict that the local heterogeneity of the outermost RuCX surface promotes the bifunctional HER mechanism by providing catalytic sites for both H adsorption and facile water dissociation.