<p>Proton exchange membrane fuel cells (PEMFC) have garnered significant amounts of attention across various industries due to their high power density levels and eco-friendly characteristics. Particularly in heavy-duty applications, such as medium- and heavy-duty commercial vehicles, multi-stack systems, are being implemented to meet higher power demands. However, stacking multiple fuel cell modules exacerbates thermal gradients and undermines the heat-rejection efficiency during high-load operation. Consequently, dynamic flow regulation and advanced temperature control algorithms are imperative to maintain the isothermal stack operation and to ensure system reliability. This study analyzes the impact of different cooling flow paths—series, parallel, and series–parallel—on the thermal management performance and on energy consumption outcomes. Additionally, a power distribution control strategy is applied in the series cooling path for a precise evaluation of these metrics. It was found that the series cooling configuration with power distribution control held the temperature variation between the stacks within 2%, effectively mitigating the issue of a load concentration in a specific stack. Furthermore, the reduction in the thermal management energy consumption was 23.23%, and the stack's net energy reduction was 1.38%. This study contributes to establishing design strategies for stable operation and improved thermal management efficiency in multi-stack fuel cell systems.</p>