<p>Vibration control in flexible-link manipulator (FLM) systems typically treats "vibration excitation reduction" as an open-loop planning issue (e.g., input shaping) while regarding "vibration suppression" as a feedback control task, leaving these two objectives often decoupled and lacking systemic integration. Addressing the scarcity of studies that resolve vibration excitation within a unified controller framework—specifically in a closed-loop manner—this paper proposes a dual-subsystem collaborative control (DSCC) framework that integrates closed-loop vibration excitation reduction with active vibration suppression. Within this unified framework, the joint angle subsystem generates smooth driving torques and constrains the amplitude of joint angle oscillations to intrinsically mitigate the excitation of flexible vibrations within the closed-loop feedback, all while ensuring trajectory tracking; concurrently, the flexible state subsystem works collaboratively to actively suppress residual vibrations. Based on Lyapunov theory, the stability of the entire closed-loop system, including flexible states, is rigorously proved. To validate the strategy’s capability in handling complex dynamic coupling, a spatial two flexible-link manipulator (STFM) is selected as the simulation object. Unlike typical planar models, this system features strong inter-joint coupling. Simulation results demonstrate that, even under strong coupling, this integrated strategy significantly reduces vibration excitation without external planning. Furthermore, tests under varying control gains and model parameter perturbations verify the superior parameter adaptability and robustness of the proposed method.</p>