A new wind-resistant design optimization method for twin towers by utilizing link bridges, named as the Modal Substructure (MSS) method, is proposed. The MSS method combines the benefits of engineering design approaches and theoretical analysis methods to achieve efficient wind-induced vibration control tailored to specific twin tower projects. The method involves three main steps: (1) establishing control objectives based on the wind-induced response characteristics of the twin towers, (2) determining control strategies by analyzing the modal acceleration characteristics of the twin towers, and (3) performing parameter optimization of the link bridge, including assessing the damping ratio, mass ratio, and frequency ratio of the bridge. By applying the MSS method, optimal configurations for the link bridge can be identified, leading to effective vibration reduction effects. The wind-induced responses of the twin towers exhibit three distinct types: predominance of out-of-phase response, predominance of in-phase response, and equal importance of in-phase and out-of-phase responses. Each response type necessitates the implementation of specific control strategies. We propose a two-section link bridge design approach: the upper section functions as a tuned mass damper to effectively control the in-phase response, while the lower section is designed as a “stiffness + damping component” to reduce the out-of-phase response.