This study presents a new method of system modeling by using the Discrete Fourier Transform for the position control system of DC Motor. And the proposed method is similar to the method of System Identification by analysis of correlation of the measured input-output data. The measured output signals are transformed to the frequency domain using DFT. The Fourier Spectrum of the transformed signals is used for knowing to the feature of having an important effect on the system. And transfer function of the second order system is estimated by the dominant parameter which is computed in the magnitude and the phase of Fourier spectrum of the transformed signals. In addition, the output signal includes the unique feature of system. So, although the basic parameter of the system is unknown for us, the proposed method has an advantage to system modeling. And the controller is easily designed by the estimated transfer function. Thus, in this paper, the proposed method is applied to the system modeling for the position control system of DC Motor and the PD-controller is designed by the estimated model. And the efficiency and the reliability of the proposed method are verified by the experimental result.