In this study, ground motion acceleration time history was decomposed into multi-band wavelet components using the wavelet multi-resolution analysis method, and a dynamic response formula for an inter-story isolation structure under earthquake action was deduced using the complex modal method. The resulting seismic signals and displacement energies in a distinct frequency channel are discussed. The impact of earthquake energy distribution in the time-frequency domain on structural response was analyzed using wavelet time-frequency analysis tools, which provide a method of analyzing the nonlinear response of inter-story isolation structures. Finally, the elastic and elastoplastic responses of a typical inter-story isolation structure under earthquake excitation are analyzed using wavelet analysis. The results show that the elastic response can be the superposed seismic response of each wavelet component. Therefore, energy concentration of earthquake ground motion in the time domain can cause an adverse effect on inter-story isolation structures.