To attain the optimal shape of the robot arm with the minimum compliance and the suitable weight and lower the possibility of vibration, this paper applies the homogenization method to describe the topology optimization design of the wafer handling robot arm which modal analysis is carried out subsequently. We deduce and establish the mathematical model of the topology optimization based on the homogenization method and calculate it by ANSYS. The results suggested that the compliance and the weight were reduced. Then we calculated the modal analysis of the optimized and non-optimized robot arms, and it was found that the first sixth natural frequencies of the optimized robot arm all increased whereas the probability of the natural vibration declined. It is concluded that the topology optimization design of the wafer handling robot has been shown to be effective in improving the stability of the robot arm.