A method for structural optimization design of wafer handling robot is presented. The static deformation of the end effector is employed as the constraint of the method. The nature frequencies of the rigid links flexible joints system are selected as the optimization objectives, and the thicknesses of the arms are determined as the optimization parameters. The dynamic model of the rigid links and flexible joints is established, and the modal analysis is carried out to determine the orders of the modal which will influence the trajectory precision. The masses of the second arm and the third arm are selected as the optimization parameters by the sensitive analysis of the nature frequencies. The deflection model of the arm is established with the variables of the thicknesses of the arm. The relationships between the thicknesses and the deformation of the end effector are analysed, and the structures of the arms are optimized based on the analysis. The comparison between the performance before optimization and the performance after optimization are carried out, and the result shows that the nature frequencies and the frequency of the vertical vibration are significantly enhanced and the deflection of the end effector is obviously reduced.