Morphing aircraft are able to keep optimal performance in diverse flight conditions. However, the change in geometry always leads to challenges in the design of flight controllers. In this paper, a new method for designing a flight controller for variable-sweep morphing aircraft is presented—dynamic inversion combined with L1 adaptive control. Firstly, the dynamics of the vehicle is analyzed and a six degrees of freedom (6DOF) nonlinear dynamics model based on multibody dynamics theory is established. Secondly, nonlinear dynamic inversion (NDI) and incremental nonlinear dynamic inversion (INDI) are then employed to realize decoupling control. Thirdly, linear quadratic regulator (LQR) technique and L1 adaptive control are adopted to design the adaptive controller in order to improve robustness to uncertainties and ensure the control accuracy. Finally, extensive simulation experiments are performed, wherein the demonstrated results indicate that the proposed method overcomes the drawbacks of conventional methods and realizes an improvement in control performance.