To meet the high precision demand of friction stir welding (FSW) for high strength large parts with complex surface,a heavy load FSW robot is developed. In order to make the robot have large working space and dexterous operation ability, the serial mechanism is chosen as the robot configuration, and the design and stiffness checking method of the high precision mechanism under heavy load are elaborated. Dynamic model of the wrist joint with clearance is deduced, and the dual motor backlash elimination control method is proposed. Backlash elimination effect simulations for different loads and bias currents are carried out, and the results show that the active backlash elimination method can effectively suppress the position fluctuation and error caused by the transmission backlash. Furthermore, in order to eliminate the deflection deformation of the z axis under the action of self weight and welding force, a deflection active compensation method is proposed, and the dynamic model and control strategy are constructed. The simulation results show that the trajectory errors caused by deflection deformation can be quickly and effectively suppressed by the deflection compensation system. The FSW robot prototype experiment shows that the robot can realize high precision trajectory control under heavy load.