Addressing the safety challenges of hydrogen fuel system (HFS) in hydrogen rail transit, this study established a high-fidelity three-dimensional CFD model based on the COMSOL Multiphysics platform to elucidate the spatiotemporal distribution characteristics of high-pressure hydrogen leakage. Under natural ventilation, buoyancy dominated hydrogen dispersion, reaching the theoretical lower flammability limit (volume fraction 0.04) within 25 s at a point 25 cm from the leak source. After 600 s, localized hydrogen volume fractions exceeded 0.1 near the enclosure roof. Horizontal diffusion rates were significantly higher than downward vertical diffusion. Forced ventilation at speeds 1 m/s effectively suppressed hydrogen accumulation risks, maintaining volume fractions below 0.04 throughout the domain. At increased ventilation speeds of 5 m/s and 10 m/s, the primary hydrogen accumulation zone shifted towards the exhaust vents, accompanied by a significant reduction in spatial concentration gradients. The research demonstrates that equipping HFS with forced ventilation systems effectively mitigates localized hydrogen concentrations. Hydrogen sensors should be prioritized within 25 cm of valve/pipe interfaces to shorten early warning time. Enclosure structural optimization is recommended to eliminate dead zones prone to gas accumulation, particularly at roof corners. These findings provide critical theoretical foundations and design guidance for ventilation system design, sensor optimization, and structural safety enhancements of HFS in hydrogen rail applications.