The servo control system based on DSP and FPGA can meet the requirements of complex controlling arithmetic. By analyzing the functions and features of DSP chip from ALTERA Co. and FPGA chip from FPGA Co. and integrating the communication between CAN bus and upper computer, a tracking controller is designed based on DSP, FPGA and CAN bus. And its function and hardware structure as well as software flow design are described. Its hardware source selection, operation principle, basic function module construction and algorithm realization modes are emphasized. The controller can meet the requirements of high-speed tracking servo system on the areas of real time, accuracy and stability and has good functional extendibility.