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This paper considers the robust output regulation and output constraints of the flexible wing system, under an output disturbance, distributed disturbances, boundary disturbances and a reference. The measurable outputs are merely the in-domain tracking error and the in-domain displacement perturbed by an unknown output disturbance that is used to define the uncertain output constraint. All the above disturbances and reference are supposed to be from an exosystem with unknown initial values. Under the guideline of internal model principle, a PDE-ODE coupled observer is designed to exponentially estimate the states of the wing system and exosystem, and meanwhile guarantee the robustness to the unknown coefficients of the disturbances, reference and output constraint. Observer-based nonlinear controllers are then proposed for the flexible wing system so that the in-domain tracking error is regulated toward zero. Furthermore, the approximately known endpoint tracking errors are further restrained by the estimation of the constraint. A numerical simulation is used to indicate the effectiveness of the designed observer-based dynamic controls. This paper also presents the advantages over the adaptive control and active disturbance rejection control. • A PDE-ODE coupled observer is designed to exponentially estimate the states of the wing system and exosystem, and further gives the approximate values of the endpoint tracking errors and output constraint. • Observer-based nonlinear controllers are proposed to guarantee the robust ourpur regulation of the in-domain tracking error of the flexible wing system. • The approximately known endpoint tracking errors are further restrained by the estimation of the unknwon constraint, which is further proved to be robust to unknown disturbances and references. [ABSTRACT FROM AUTHOR]