This paper discusses an approach to apply visual servoing to a 3D flexible-link manipulator. The proposed approach is composed of an end-effector position control based on eye-in-hand visual servoing and a vibration suppression control. In order to decouple the end-effector position control and the vibration control, the end-effector position control is applied in a low frequency domain, while the vibration control is applied in a high frequency domain. To decouple the frequency domain, a high-pass filter and a low-pass filter are used. Stability of the whole system is analyzed by investigating the pole of the system. Using the proposed approach, the 3D flexible-link manipulator succeeds to insert a peg into a hole whose clearance is 0.5mm. However, it is difficult for the flexible-link manipulator to insert the peg into a hole whose clearance is 0.1mm, if there is no force control. Therefore, an impedance control is also tested together with the end-effector position control and the vibration control. Using the modified approach, the flexible-link manipulator succeeds to insert the peg into the hole whose clearance is 0.1mm.