Flexible air-breathing hypersonic vehicles feature significant uncertainties which pose huge challenges to robust controller designs. In this paper, four major categories of uncertainties are analyzed, that is, uncertainties associated with flexible effects, aerodynamic parameter variations, external environmental disturbances, and control-oriented modeling errors. A uniform nonlinear uncertainty model is explored for the first three uncertainties which lumps all uncertainties together and consequently is beneficial for controller synthesis. The fourth uncertainty is additionally considered in stability analysis. Based on these analyses, the starting point of the control design is to decompose the vehicle dynamics into five functional subsystems. Then a robust trajectory linearization control (TLC) scheme consisting of five robust subsystem controllers is proposed. In each subsystem controller, TLC is combined with the extended state observer (ESO) technique for uncertainty compensation. The stability of the overall closed-loop system with the four aforementioned uncertainties and additional singular perturbations is analyzed. Particularly, the stability of nonlinear ESO is also discussed from a Lienard system perspective. At last, simulations demonstrate the great control performance and the uncertainty rejection ability of the robust scheme. (C) 2014 Published by Elsevier Ltd. on behalf of IAA.