An adaptive Fourier Transform (FT) with an optimal window has been proposed for the time-frequency analysis of nonstationary time series. The method allows for a good estimation of both frequency and amplitude of the spectrum and can be easily applied to the general case of time-varying signals. The evaluation of the proposed approach has been performed on measured time-varying signals from a suspension bridge model and a steel frame model whose data have the typical non-stationary characteristics. The numerical results show that the proposed approach can overcome some of the difficulties encountered in the classic Fourier transform technique and can achieve higher computation accuracy.