The hypersonic waverider using the morphing configuration can improve the overall performance and broaden the flight range. On the other hand, the hypersonic waverider belongs to the lightweight construction, leading to the presence of the intrinsic elasticity. As a result, the integrated consideration of the active deformation and elastic action is important for the morphing waverider to realize global optimization. In this paper, the contro-integrated design methods are proposed for the morphing waverider to implement the trade-off analysis between the active deformation and intrinsic elasticity. First, the parametric model is built to describe the hypersonic flight characteristics. Then, the elastic dynamics is introduced to quantify the coupling responses associated with the angle of attack and elevon deflection. Furthermore, the integrated design is considered for the active deformation and inherent elastic action, and also the control law is designed to suppress the active and passive morphing disturbances. Finally, the simulation is conducted to test the effectiveness of the presented methods for the morphing waverider.