To improve safety of missile weapon systems, and based on ascertaining affecting factors of human operating, establish human fault analysis model of missile weapon system based on Bayesian network. Introduce Bayesian network, discuss the human fault influence factor and mechanism. Through example analysis, combine expert experience and knowledge to establish model and evaluate equipment human fault probability. The result shows that the human fault probability and equipment statistic data were conform by analysis method. The quantitative evaluation model is correct and effective.