This study investigates the flight longitudinal tracking control problem of hypersonic vehicle in presence of the input saturation, external disturbances, model parametric uncertainties, and actuator faults. First, the velocity and altitude subsystem are established with disturbances based on the feedback linearization model. Second, two robust anti-saturation fault-tolerant controllers are designed for the velocity subsystem and altitude subsystem by the utilization of the tangent function, Nussbaum function, and adaptive nonlinear filter. Finally, Lyapunov stability theory is used to prove that the states of the closed-loop system are bounded. And, the effectiveness and robustness of the control strategy are proved by numerical simulations.