Hydrogen production from water electrolysis is an important way of renewable energy consumption, driven by “dual-carbon” targets. The proton exchange membrane (PEM) electrolyzer has become the preferred equipment for coupling with wind power, photovoltaic, and other intermittent renewable energy sources due to its fast start-stop response, high energy efficiency, and strong adaptability. In this paper, we propose a PEM array optimization strategy that combines “segmental regulation” and “rotation control,” considering the system’s hydrogen production efficiency and equipment life management. Simulation results indicate that this strategy can enhance the overall hydrogen production efficiency of the system, effectively equalizing the operating load and start-stop frequency of each electrolyzer, thereby extending equipment life and improving the stability and economy of the system. The research results can provide a theoretical basis and practical reference for the efficient scheduling and operation management of renewable energy hydrogen production systems.