It is known that the flexibility and programmable abilities have made the FPGA widely used as controllers to the electrical machines and systems. Above all, the high density of recent developed chip results in many of the CPU cores and complicated hardware can be programmed into the chip to be as controller. Thus, this topic is based on the currently available technologies of FPGA-based system design to the parallel processing. Software and hardware co-design are shown to reach the performance, and the system’s software stream data are processed with the hardware parallel technique. This analysis enables FPGA-based control system on the parallel computing platform to achieve the simultaneous operation for 3-axis motor motion and drive system control. In that way, we chose the high density FPGA, Altera Cyclone II EP2C8Q208C8N, as the chip to develop the hardware of microprocessor, motor drive and motion controller. The developed system was practically applied to a 3-axis motion platform driven by stepping motors to evaluate the system performance.