Abstract: >This paper investigates the vibration control problem of a flapping-wing unmanned aerial vehicle (UAV) with a coupled rigid-flexible wing and input saturation. The flapping-wing UAV is modeled as a hybrid partial-ordinary differential equation by analyzing the coupled dynamics between the rigid and non-homogenous flexible wings. Boundary control is implemented at the UAV body and the connection point of the rigid and flexible wings to suppress the bending and torsional deformations of the flexible wings and simultaneously adjust the attitude angle. An active disturbance rejection control (ADRC) method is employed to design an extended state observer with time-varying gain to estimate external disturbances online in real-time and subsequently counteract their effects in the negative feedback loop. An auxiliary system is constructed to address input saturation nonlinearities. The Lyapunov stability theory is applied to demonstrate that the active disturbance rejection boundary vibration control scheme designed in this paper can ensure the exponential stability of the closed-loop system. Simulation experiments show that the proposed control scheme can achieve vibration suppression and attitude tracking simultaneously.