The seismic wave input has an important influence on the nonlinear response of a structure. Selecting and inputting appropriate seismic waves for calculation are the primary conditions that must be considered to ensure accurate results for the time- history analysis of a structure. This paper optimizes and proposes a wave selection method that considers the time- frequency characteristics of seismic waves by comparing different modeling methods for the instantaneous spectrum of the seismic wave. Results show that the proposed wave selection method matching of the instantaneous spectrum can effectively control the difference between various selected seismic waves in time and frequency domains and reduce their response dispersion of the time- history analysis of structure, thereby providing a basis for wave selection in actual projects.