In order to suppress vibration of the flexible-joint manipulator, a new topological structure of the manipulator with the controllable local degrees of freedom is suggested. By kinematic and dynamic analysis, it is found that arbitrary motions introduced by the controllable local degrees of freedom are independent of the nominal end-effector motion, but can greatly affect dynamic performance of the manipulator. As a result, a vibration control strategy is put forward based on the controllable local degree of freedom. By planning the branch link motion, the vibration of the flexible-joint manipulator can be reduced. The results of numerical simulations verify the effectiveness of the vibration control strategy proposed in this paper.