The state-of-the-art active HER catalysts in acid media (e.g., Pt) generally lose considerable catalytic performance in alkaline media mainly due to the additional water dissociation step. To address this issue, synergistic hybrid catalysts are always designed by coupling them with metal (hydro)oxides. However, such hybrid systems usually suffer from long reaction path, high cost and complex preparation methods. Here, we discover a single-phase HER catalyst, SrTi0.7Ru0.3O3-δ (STRO) perovskite oxide highlighted with an unusual super-exchange effect, which exhibits excellent HER performance in alkaline media via atomic-scale synergistic active centers. With insights from first-principles calculations, the intrinsically synergistic interplays between multiple active centers in STRO are uncovered to accurately catalyze different elementary steps of alkaline HER; namely, the Ti sites facilitates nearly-barrierless water dissociation, Ru sites function favorably for OH* desorption, and non-metal oxygen sites (i.e., oxygen vacancies/lattice oxygen) promotes optimal H* adsorption and H2 desorption.