The slow water dissociation is the rate-determining step that slows down the reaction rate in alkaline hydrogen evolution reaction (HER). Optimizing the surface electronic structure of the catalyst to lower the energy barrier of water dissociation and regulating the binding strength of adsorption intermediates are crucial strategy for boosting the catalytic performance of HER. In this study, RuO2/BaRuO3 (RBRO) heterostructures with abundant oxygen vacancies and lattice distortion were in-situ constructed under a low temperature via the thermal decomposition of gel-precursor. The RBRO heterostructures obtained at 550 °C exhibited the highest HER activity in 1 M KOH, showing an ultra-low overpotential of 16 mV at 10 mA cm−2 and a Tafel slope of 33.37 mV dec−1. Additionally, the material demonstrated remarkable durability, with only 25 mV of degradation in overpotential after 200 h of stability testing at 10 mA cm−2. Density functional theory calculations revealed that the redistribution of charges at the heterojunction interface can optimize the binding energies of H* and OH* and effectively lower the energy barrier of water dissociation. This research offers novel perspectives on surpassing the water dissociation threshold of alkaline HER catalysts by means of a systematic design of heterogeneous interfaces.