The design of a robust longitudinal flight controller for the air-breathing hypersonic vehicle is presented in this paper. The non-standard dynamic characteristics of air-breathing hypesonic flight vehicles together with the aerodynamic effects of hypersonic flight make the flight control of such systems highly challenging. Moreover the wide range of speed during operation and the lack of a broad flight dynamics database add significant plant parameter variations and uncertainties to the vehicle modeling and control problem. In this paper, these features was modeled as uncertainties and incorporated into the design procedure of a flight control system by mu-synthesis techniques. And the uncertainty in detailed manner was not modeled, but rather to lump all of these effects together into one full-block uncertainty at the input of a four-state, nominal model of the vehicle. The results illustrated that mu-synthesis is ideal for addressing the problem of multiple uncertainty sources present in air-breathing hypersonic flight control system.