Civil aircraft system functional hazard assessment refers to the process of systematic comprehensive analysisof the system function, namely according to system function failure condition to evaluate severity influence on the safety of aircraft, so as to realize the function of the level of recognition and classification process, which is the top key system design process. Based on the analysis of a large number of relevant materials and practical experience, this article gives the ideas and methods which applies to commercial fly-by-wire flight control system'sfunction definition, function of failure condition, analysis and validation of the functional failure affect level, and makes sure that correctness and completeness of fly-by-wire flight control system FHA. The method has been applied to a commercial fly-by-wire flight control system of the evaluation work of FHA.