To improve the dynamic tracking ability of spot welding manipulator with heavy payload, a new programmable motion controller, which can provide software and hardware supports for several kinds of control algorithms, is developed first. Then, a decentralized adaptive control algorithm is used to compensate the coupling between the manipulator joints, and the algorithm is easy to implement based on the motion controller. Finally, experiments demonstrate that, compared with the traditional PID, the dynamic tracking ability of the manipulator can be obviously improved with this algorithm.