The rapid development of hydrogen refueling station (HRS) has induced potentially serious risk exposure to public safety. Consequently, the safety issues associated with HRS have become a research hotspot. A comprehensive methodology for risk analysis of hydrogen facilities was proposed. A failure tree analysis (FTA) was used for hazard analysis while a bow-tie diagram and Bayesian network were applied to model the worst-case accident scenario and to analyse the risks of root event. In addition, the fuzzy set theory combined with FTA was employed to calculate the failure probability of the hydrogen facilities. The risk analysis of a HRS was implemented with the proposed method. The results showed that the vapour cloud explosion (VCE) of compressors in the gas HRS was the most risky scenario with the probability of 8.12E–04 before taking safety measures. The death, severely injured, and minor injured radius of the VCE from compressors was 35.5, 20.0, and 10.3 m, respectively. Results also revealed that after taking several safety barriers, the risk level converted from an intolerable risk level to a tolerable risk with control level.