Abstract Downsizing a catalyst nanoparticle (NP) to a single atom (SA) has proven to be highly effective in increasing catalytic activity and decreasing the amount of catalyst required for various electrochemical reactions. However, insufficient stability of the single‐atom site catalysts (SACs) is still a significant challenge for their practical application. Here, SACs firmly bound to stable metal oxide NPs are proposed to dramatically increase the electrochemical activity and stability of SA‐based catalysts for hydrogen evolution reaction (HER). Starting from a Ru‐infiltrated, Zr‐based metal‐organic framework (MOF), the tetragonal zirconium oxide (ZrO 2‐x ) NPs‐embedded carbon matrix is fabricated as support through facile pyrolysis. Simultaneously, Ru SAs as active sites are well dispersed on the surface of ZrO 2‐x NPs due to the generation of oxygen vacancies in the tetragonal ZrO 2‐x . The Ru‐ZrO 2‐x SAC exhibits a 4–5 times higher mass activity than commercial Pt and Ru catalysts and superior durability due to strong metal‐support interaction (SMSI) between Ru atoms and ZrO 2‐x substrate.