Hydrogen-powered unmanned aerial vehicles (UAVs) offer significant advantages, such as environmental sustainability and extended endurance, demonstrating broad application prospects. However, the hydrogen fuel cells face prominent thermal management challenges during flight operations. This study established a numerical model of the fuel cell thermal management system (TMS) for a hydrogen-powered UAV. Computational fluid dynamics (CFD) simulations were subsequently performed to investigate the impact of various design parameters on cooling performance. First, the cooling performance of different fan density configurations was investigated. It was found that dispersed fan placement ensures substantial airflow through the peripheral flow channels, significantly enhancing temperature uniformity. Specifically, the nine-fan configuration achieves an 18.5% reduction in the temperature difference compared to the four-fan layout. Additionally, inlets were integrated with the fan-based cooling system. While increased external airflow lowers the minimum fuel cell temperature, its impact on high-temperature zones remains limited, with a temperature difference increase of more than 19% compared to configurations without inlets. Furthermore, the middle inlet exhibits minimal vortex interference, delivering superior thermal performance. This configuration reduces the maximum temperature and average temperature by 9.1% and 22.2% compared to the back configuration.