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In the process of re-entry of hypersonic flight vehicle, attitude control model is a complex object of fast time-varying parameters of a wide uncertain range. This paper design fractional order PID controller to increased the complexity of the controller designed using modern control methods. Fractional order PID (FOPID) controller inherits the advantages of the traditional PID controller and has stronger robustness and better control quality. In this paper, Fractional order PID controller is achieved by optimal Oustaloup digital algorithm and based on time-varying nonlinear model of hypersonic flight vehicle. Use D-decomposition to analyze the affect to Mach number and angle of attack stability region caused by the order of Fractional order PID. Simulation results show that Fractional order PID controller not only improves the control quality, but also is not sensitive to the changes of system parameters, the stability of hypersonic flight vehicle can be achieved within a wide range.