In this paper, for the six-degree-of-freedom (six-DOF) model of hypersonic flight vehicle (HFV) subject to actuator faults, state constraints, parametric uncertainties, and external disturbances, an adaptive fault tolerant control (FTC) scheme is proposed based on barrier Lyapunov functions (BLFs). The study is begun with a series of control-oriented manipulations: at first, due to the high complexity of the six-DOF model, the corresponding simplified model is proposed under reasonable assumptions; then, through the stability analysis of the internal dynamics, we can conclude that the vehicle model is a non-minimum phase system, namely, having unacceptable zero-dynamics. In order to solve the non-minimum phase problem, the elevator-to-lift coupling term is regarded as uncertainty of the model. Subsequently, in consideration of the insufficient control torque caused by the fault of the rudder or elevators, an adaptive fault-tolerant controller is designed based on BLFs, backstepping method, and Nussbaum gains. In the control law, the uncertain parameters are replaced by their estimates updated by adaptive laws. And the angle of attack and the roll angle of the aircraft are constrained in the preset range. Additionally, the convergence of the proposed FTC algorithm and the boundedness of all the signals of the closed system is proved by Lyapunov stability theory. At last, the numerical simulation results of the six-DOF model are carried out to manifest the effective tracking performance of the proposed FTC scheme.