<p>In addition to lightweight and high load-bearing capacity, certain scenarios in aerospace field place further requirements on thin-walled structures, particularly double-skin stiffened structures, such as low moment of inertia and high flutter resistance. A concurrent stiffener-skin topology optimization method is proposed to enhance stiffness and reduce weight, while suppressing flutter by considering constraints on external aerodynamic shape and modal characteristics. The stiffener layout is optimized using the adaptive growth method, inspired by natural branch systems, while skin thickness is optimized through geometry optimization with material interpolation. A dual nodal system model is developed to maintain external shape by offsetting skin elements inward and allowing adaptive changes in stiffener geometry. Additionally, partitioned mass center location constraint is introduced as an indirect scheme to control mode shapes, aiming to achieve modal decoupling. Applied the method to a rudder structure, a tree-like stiffeners and tree crown-like skins are obtained, and the optimized rudder structure shows enhanced static–dynamic performance and greatly reduced moment of inertia. Furthermore, the coupling degree of bending-torsion modes is lowered, leading to a notable increase of the forecast flutter frequency. This method innovatively introduces a dual nodal model to avoid component overlaps and integrates variable thickness skin to balance stiffness and mass distribution, combining multiple components for concurrent topology optimization. The approach highlights the importance of integrative stiffness-mass-mass center design in decoupling bending-torsion modes, which in turn suppresses flutter, and offers a flexible and universal solution for the design of high-performance thin-walled structures.</p>