The work aims to eliminate the elastic vibration of the flexible manipulator and ensure the stable operation of the manipulator. With the horizontally moving single-link flexible manipulator as the study object, a dynamic model was established, based on which the dynamic equation was decomposed into slow and fast sub-systems in the singular perturbation method. These two sub-systems were controlled respectively by means of back-stepping sliding mode variable structure and fuzzy control. Finally, ADAMS and MATLAB software were used for joint simulation to comparatively analyze the control results and the traditional PID control. The stability time, vibration quantity, angular velocity and control moment were all improved. Compared to traditional PID control, the stability time of such control mode was shortened by 75%. The results show that this control method is good for vibration control of flexible manipulator, and the control effect is significantly better than the traditional PID control.