In the previous research, dynamic results have been analyzed in the time and frequency regions. Time and frequency region can be transformed by the Fourier transform. This transform is very useful about analyzing system behaviors. However, because of coupling, it cannot give clear results in the real system including lots of defects. In this paper, we introduced the analysis based on quefrency region to represent physical means clearly from complicated results. We simulated the drive train system which has defects, and compared between frequency and quefrency region to show its excellence. To do this process, We established mathematical model. The equation of motion was derived by the Lagrange equation and constraint equations. The constraint equation included relationships about gear mesh, flexibility of shaft. About numerical analysis, the Newmark beta method was used to get results. And FFT (Fast Fourier Transform) which converts results from time domain to frequency, qufrequency was used.