By rationally adjusting the coordination environment and constructing the more electron‐enriched active site in single‐atom catalysts, the effect of heterogenous peroxymonosulfate (PMS)‐based Fenton‐like reactions can be effectively improved, yet remains a severe challenge. In this study, the electron‐rich Ru dual‐atom site is successfully immobilized onto N‐doped carbon (Ru2N6‐C) for PMS activation in water purification. The presence of electron‐rich Ru dual‐atom sites not only provides more electrons for PMS but also facilitates the formation of a Yeager adsorption configuration on the catalyst surface, which enhances O─O bond cleavage and leads to an increase in •SO4− and •OH generation. Moreover, the Ru2N6‐C catalyst exhibits exceptional durability and reliability, achieving an ultra‐high efficiency with a turnover frequency of 153.95 min−1 M−1 for the naproxen degradation. A membrane reactor is further developed for the purification of wastewater, which is expected to provide a viable approach to controlling water pollution through the design of metal dual‐atom sites carbon‐based catalysts.