Proton exchange membrane fuel cells (PEMFC) are an important development direction in the future transportation field. However, in the real-time dynamic operation of PEMFC system, stack temperature and humidity are a pair of strongly coupled variables, which limit improvements in system output performance. To address this challenge, this paper proposes a performance optimization method for PEMFC power generation system based on dual-closed-loop active disturbance rejection control (DCLADRC). To accurately reflect the output performance under various temperature and humidity conditions, a nonlinear dynamic model of PEMFC is established. By testing the net power characteristics of the PEMFC system under different load currents, the optimal control values of temperature and humidity are derived. The experimental verification results show that DCLADRC effectively improves the output performance of the PEMFC system.