Maximizing the catalytic activity of single-atom catalysts is vital for the application of single-atom catalysts in industrial water-alkali electrolyzers, yet the modulation of the catalytic properties of single-atom catalysts remains challenging. Here, we construct strain-tunable sulphur vacancies around single-atom Ru sites for accelerating the alkaline hydrogen evolution reaction of single-atom Ru sites based on a nanoporous MoS2-based Ru single-atom catalyst. By altering the strain of this system, the synergistic effect between sulphur vacancies and Ru sites is amplified, thus changing the catalytic behavior of active sites, namely, the increased reactant density in strained sulphur vacancies and the accelerated hydrogen evolution reaction process on Ru sites. The resulting catalyst delivers an overpotential of 30 mV at a current density of 10 mA cm−2, a Tafel slope of 31 mV dec−1, and a long catalytic lifetime. This work provides an effective strategy to improve the activities of single-atom modified transition metal dichalcogenides catalysts by precise strain engineering.