RuO2 with high intrinsic activity for water oxidation is a promising alternative to IrO2 in proton exchange membrane (PEM) electrolyzer, but it suffers from long-term stability issues due to overoxidation. Here, we report a sub-4 nm Ru-RuO2 Schottky nanojunction (Ru-RuO2-SN) prepared by a microwave reaction that exhibits high activity and long-term stability in both three-electrode systems and PEM devices. The lattice strain and charge transfer induced by the metal-oxide SN increase the work function of the Ru-RuO2-SN, optimize the local electronic structure, and reduce the desorption energy of the metal site to the oxygen-containing intermediates; as a result, it leads to the oxide path mechanism (OPM) and inhibits the excessive oxidation of surface ruthenium. The Ru-RuO2-SN requires only 165 mV overpotential to obtain 10 mA·cm-2 with 1400 h stability without obvious activity degradation, achieving a stability number (6.7 × 106) matching iridium-based catalysts. In a PEM electrolyzer with Ru-RuO2-SN as an anode catalyst, only 1.6 V is needed to reach 1.0 A·cm-2 and it shows long-term stability at 100 mA·cm-2 for 1100 h and at 500 mA·cm-2 for 100 h. The reaction mechanism for the high stability of Ru-RuO2-SN was analyzed by density functional theory calculations. This work reports a durable, pure Ru-based water-oxidation catalyst and provides a new perspective for the development of efficient Ru-based catalysts.