This paper proposes a fast Fourier transform(FFT)-based spectral analysis method(SAM) for the dynamic responses of the linear discrete dynamic models with non-proportional damping. The SAM was developed by using discrete Fourier transform(DFT)-theory. To verify the proposed SAM, a three-DOF system with non-proportional viscous damping is considered as an illustrative example. The present SAM is evaluated by comparing the dynamic responses obtained by SAM with those obtained by Runge-Kutta method.