[Objectives] To address the poor operational stability and high unit hydrogen production cost caused by strong power fluctuations of wind and photovoltaic (PV) renewable energy, this study investigates an optimized control strategy for a dual-channel hybrid hydrogen production system under wind-PV coupled application scenarios. [Methods] An optimized control strategy for a dual-channel electrolytic cell system based on ensemble empirical mode decomposition (EEMD) and Petri net-based start-stop correction is proposed. Wind and PV power signals are decomposed using EEMD, and power components at different frequency bands are allocated to alkaline and proton exchange membrane (PEM) electrolytic cells according to their dynamic response characteristics. Meanwhile, a Petri net model is employed to construct start-stop logic for electrolytic cells, effectively suppressing frequent switching under low-load conditions. Furthermore, a multi-objective optimization model is established with the objectives of maximizing system energy conversion efficiency and minimizing the unit hydrogen production cost, which is solved using a multi-objective particle swarm optimization algorithm. [Results] Simulation results based on measured wind-PV power output data from the Zhangbei region indicate that the optimized hybrid hydrogen production system achieves an energy conversion efficiency of 58.64% and a unit hydrogen production cost of 2.3958 USD/kg. Compared with conventional single-type hydrogen production schemes, the proposed method improves efficiency by 15.25% and reduces cost by 1.7384 USD/kg, while significantly decreasing the number of start-stop events of electrolytic cells. [Conclutions] The results demonstrate that the proposed control strategy effectively enhances system stability and reduces economic cost, providing a practical and feasible optimization approach for the efficient operation of wind-PV hydrogen production systems.