This paper describes system modeling and controller design method in the measured signal by discrete Fourier transform. 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 measured signal. In addition, the controller was designed by the estimated transfer function, and the results were compared. The proposed estimation method of transfer function contains only a very simple mathematical process. Therefore, it is effective to design the controller in the measured signal when the output of the system contains the characteristics of complex exponential functions case. The proposed method was applied on Op-Amp system to verify the efficiency and the reliability. The results show that the proposed algorithms are highly applicable to the system modeling and controller design in the measured data.