During the processing of wafer, in order to avoid the friction between wafer and wafer box, and to guarantee the clean state of the working environment simultaneously, small contour error and little vibration are required for wafer transfer robot to deliver wafer, i.e., to achieve stable and accurate trajectory for wafer delivery. To lessen contour error, suppress vibration, a kind of control algorithm has been proposed in this paper combining cross-coupled synchronized control and input shaping. Via cross-coupled synchronized control, synchronization of the actuating joint can be improved and the contour accuracy can be enhanced; through the shaping of the driving impulses for the shoulder joint and the elbow joint by input shaper, the vibration at the end-effector can be reduced. Based on the experiments verified on the planar joint wafer transfer robot, it shows that the synchronizing and vibration-suppressing performance is excellent by taking advantage of the method covering both cross-coupled synchronized control and input shaping.