Safety Assessment on civil aircraft is one of the effective methods to realize the airworthiness of aircraft. In this paper, based on the principle and method of civil aircraft system safety design and assessment, a certain high lift system is taken as an example, and functional hazard analysis and fault tree analysis are carried out for the failure condition of ’flap asymmetry motion over limit’, the critical factor affecting safety design are gained. By improving the design method of the critical factor, the system scheme which can meet the safety object is finally obtained.