The coordination chemistry of the metal-support interface largely determines the electrocatalytic performance of heterostructured electrocatalysts. However, it remains a great challenge to effectively manipulate the interface chemistry of heterostructures at the atomic level. Herein, functionalized carbon-supported Ru heterostructured electrocatalysts are designed that contain abundant Ru-N(O)-C moieties with a view towards fast hydrogen evolution reaction (HER). The coordination chemistry of the Ru-N(O)-C moieties, and hence, the geometric and electronic structures of the Ru species can be precisely modulated via an appropriate annealing treatment. Specifically, the optimal heterostructured electrocatalyst delivers the highest specific activity by far among reported Ru-based electrocatalysts, and the turnover frequency value reaches 32 s−1 at the overpotential (η) of 100 mV, which also surpasses the state-of-the-art Pt/C catalyst in alkaline media. The interface engineering of the heterostructured electrocatalyst not only facilitates H2O adsorption and dissociation with help from the Ru-N(O)-C moieties, but also further optimizes the adsorption behavior of H on the metallic Ru species, thereby inducing accelerated hydrogen evolution kinetics in both alkaline and acidic media. The present results demonstrate the successful atomic-level interface engineering of carbon-supported Ru-based heterostructures and shed new light on the development of advanced electrocatalysts for fast hydrogen evolution, and beyond.