A motor-based decoupling and partial (input-output) linearization approach to the control of multi-link robots with joint and link flexibilities is studied in this paper. The control strategy consists of two parts: nominal tracking control and perturbed stabilization control. The nominal tracking control derived by the differential geometric structure algorithm is an input-output decoupling and partial linearization feedback law capable of precise motor-based trajectory tracking, but the zero dynamics of the unobservable nonlinear elastic subsystem remains unstable. In order to actively suppress the elastic vibrations, it is necessary to sacrifice the perfect motor-based tracking capability somewhat by introducing a perturbation control in the vincinity of a desired trajectory. The perturbed stabilization control synthesized by combined LQR and servocompensator is used to achieve active damping of elastic vibration and robust tracking of motor dynamics. To offset the tracking errors of the end effector caused by joint and link deflections due to gravity, the quasi-static deflections can be taken into account in the trajectory planning and LQ regulator.A two-link arm is tested via simulation.