The aerodynamic configuration of large swept-back tri-wings is generally adopted for hypersonic vehicles, but the structural stiffness of the ailerons is weak, which may lead to damage due to the flutter behavior. In the initial stage of structural design, studying the flutter characteristics of tri-wing flight vehicles is necessary and can provide the stiffness index of the tri-wing structural design. To assess the flutter characteristics of tri-wing flight vehicles efficiently, a rapid modeling technique of the finite element method was used in this paper. For the structural scheme of large swept-back tri-wing flight vehicles, a structural dynamic model was modeled using the rapid modeling technique, the unsteady aerodynamic was computed using the double-lattice method, and the flutter characteristics were analyzed using the P-K method. Variable parametric studies were conducted to evaluate the effects of the stiffness of the aileron skin, the stiffness of the control mechanism, and the mass distribution of the aileron on the flutter characteristics of large swept-back tri-wing flight vehicles. The results showed that the key flutter coupling modes of such vehicles are symmetric and anti-symmetric combinations of aileron rotation and torsion. Additionally, optimizing the control mechanism stiffness and mass distribution of the aileron could improve the flutter boundary, which can be helpful in the structural design of such vehicles. The flutter optimization technique effectively improved the flutter boundary, significantly enlarged the flight envelope, and accurately provided the stiffness index for the structural design of large swept-back tri-wing flight vehicles.