As a sustainable and high-performance energy option, hydrogen energy has garnered increasing attention and support in recent years. Hydrogen energy technologies, including production, storage, transport, and utilization, have been steadily improving, and its application fields are continually expanding, encompassing transportation, energy storage, industrial manufacturing, and residential heating, among others. Notably, in the transportation sector, hydrogen-powered rail transit vehicles are gradually gaining popularity. Hydrogen refueling station safety plays a key role in supporting the reliable operation of rail transit powered by hydrogen. The construction of rail transit hydrogen refueling stations serves as the foundation for the widespread adoption of hydrogen-fueled rail vehicles. This paper, focusing on the operational safety requirements of hydrogen fueling facilities for rail transportation, selects various risk factors that affect the operational safety of these stations. By deriving calculation formulas for evaluation indicators, a Bayesian network architecture is created based on fuzzy fault tree analysis. Furthermore, calculations are performed using triangular membership functions, fuzzy subsets of failure probabilities, and posterior probability formulas, verifying the applicability of this safety risk assessment method in the actual risk evaluation of rail transit hydrogen refueling stations.