With the increase of Liquefied Natural Gas (LNG) fuel‐powered vessels, LNG bunkering vessels have become an important development direction of LNG bunkering technology for its advantages. However, the LNG bunkering vessel operation risk assessment is relatively few. Formal Safety Assessment (FSA) is a novel structured and systematic risk analysis method for Marine engineering, through the data analysis based on probability theory, people can foresee the risk before the accident and take measures to reduce the risk and avoid heavy loss. In this paper, the LNG bunkering vessel operation process is divided into four subprocesses: the loading process, the navigation process, the bunkering process, and the anchoring process. The FSA method is used to identify and evaluate the risks in each process, judge the negligible risk, reasonable and feasible low risk, unacceptable risk, and put forward corresponding safe measures to provide safety guarantees for the operation of LNG bunkering vessels. Through the standardized assessment steps of FSA, a risk model for the LNG bunkering vessel operation process is established, and reasonable suggestions and measures that can effectively control the risk of the LNG bunkering vessel operation process are proposed, the research results of this paper can provide important technical guidance and reference value for the safe operation of LNG bunkering vessel.