In this paper, we propose a boundary control strategy for vibration suppression of two flexible wings. As a basic approach, Hamilton's principle is used to ascertain the system dynamic model, which includes governing equations - four partial differential equations and boundary conditions - several ordinary differential equations. Considering the coupled bending and torsional deformations of flexible wings, boundary control force and torque act on the fuselage to regulate unexpected deformations of flexible wings. Then, we present the stability analysis of the closed-loop system through Lyapunov's direct method. Simulations are carried out by using finite difference method. The simulation experimental results illustrate the significant effect of the developed control strategies.