The novel FPGA (Field Programmable Gate Arrays) can embed a processor to be an SoPC (System-on-a-Programmable-Chip) environment which allows user to design the applications by mixing hardware and software. Therefore, a motion control system of wafer-handling robot based on the SoPC technology is presented in this paper. In FPGA, it is consists of two modules. The first module is Nios II processor which is used to realize the motion trajectory planning and three-axis position/speed controllers by software. The program developed in Nios II processor uses C language. The second module is presented to implement three-axis current vector controllers by hardware, and VHDL (VHSIC Hardware Description Language) is applied to describe the controller behavior. Therefore, a fully digital motion controller for wafer-handling robot, such as three current vector controllers, three position/speed controller and one trajectory planning are all can implemented by a single FPGA chip. Finally, an experimental system constructed by an FPGA experimental board, one three-DOF wafer-handling robot, and three inverters is set up to demonstrate the correctness and effectiveness of the proposed SoPC-based motion control system of wafer-handling robot.