In this paper, an adaptive backstepping controller of hypersonic flight vehicle (HFV) system is investigated in the presence of unknown actuator and sensor faults, unknown control direction and varying external disturbance, which expands traditional fault-tolerant control (FTC) approaches in HFV field. The control-oriented model is established with reasonable and comprehensive analysis of various fault types. Compared with the previous FTC research on HFV system, the time-varying and fixed fault types are simultaneously designed for actuator and sensors, and the control direction is unknown, which can more accurately simulate the real fault situations in the hypersonic flight environment. To avoid singularity problems caused by the unknown control direction, the Nussbaum gain function technique is adopted in the control algorithm, which is also capable of overcoming the influence of unknown time-varying fault parameters. The boundness and stability of system under the designed control scheme are theoretically verified. Finally, numerical simulation results demonstrate the effectiveness and superiority of the proposed control strategy.