For the six-degree of freedom dynamics of hypersonic flight vehicle, an autonomous reliable intelligent controller using online estimation and condition monitoring is designed in this paper. Based on model transformation, the outer-loop trajectory tracking is converted to the inner-loop attitude tracking. According to the aerodynamic model of large flight envelope and the thrust model of combined engine, the original dynamics is transformed into a switched nonlinear form. For each subsystem, neural network and nonlinear observer are employed to deal with aerodynamic uncertainty and external disturbance, while modeling errors are built to design composite update laws. Considering that the statically unstable HFV is prone to large deviation due to mode switching and wind disturbance, the condition monitoring signal with finite-time robust design is introduced to adjust control surfaces. With the average dwell time on the switching signal, the stability of the whole switched system is proved using Lyapunov approach. Simulation studies are performed to show the effectiveness of the design.