The operational performance of proton exchange membrane fuel cells (PEMFC) is highly influenced by temperature, making effective thermal management essential. However, the multivariate coupling between pumps and radiators presents significant control challenges. To address this issue, a dual DDPG-PID control strategy is proposed, integrating temperature and flow rate variations to enhance system stability and response. Simulation results demonstrate that the proposed method significantly reduces temperature control errors and improves response time compared to conventional PID-based strategies. Specifically, the D-DDPG PID achieves a temperature error reduction of up to 75.4% and shortens the average tuning time by up to 25.6% compared to PSO-PID. Furthermore, the strategy optimizes cooling system performance, demonstrating its effectiveness in PEMFC thermal management.