This paper analyzes the control surface damage of civil aircraft flight control system. Firstly, the fault feature extraction method is analyzed. Then the control surface damage is studied and it is simulated by Simulink. The fault injection is realized by setting the damage coefficient in the simulation model. It simulates seven kinds of fault modes, analyzes the simulated flight data in time domain, then getting the typical fault feature set of flight control system. At last, taking the elevator control surface damage as an example, this paper analyzes the fault characteristics of the civil aircraft flight control system. The results show that the method has good practicability.