This paper presents a dynamic modeling and a robust PID controller design process for the wire bonder head assembly. For modeling elements, the system is divided into electrical part, magnetic part, and mechanical part. Each part is modeled using the bond graph method. The PID controller is used for high speed/high accuracy position control of the wire bonder assembly. The Taguchi method is used to obtain the more robust PID gain combinations than conventional one. This study makes use of an L18 array with three parameters varied on three levels. Results of simulations and experimental show that the designed PID controller provides a improved ratio of signal to noise and a reduced sensitivity improved to the conventional PID controller.