In this paper, an online flight envelope protection system is developed and implemented on impaired aircraft with structural damage. The whole protection system is designed to be a closed loop of several subsystems, including system identification, damage classification, flight-envelope prediction, and fault-tolerant control. Based on the information given by damage classification, the flight envelopes are explicitly retrieved, processed online from the database, and fed into the fault-tolerant controller, which makes the protection system adaptive to a wide range of abnormal conditions. Simulation results show that with envelope protection, loss-of-control accidents are more likely to be prevented, since excessive commands to the controller are restricted based on the updated information of the changed flight envelopes. In this way, the fault tolerance of the impaired aircraft can be effectively enhanced.