As the selection of seismic records is very important for dynamic elasto-plastic time-history analysis of base isolated structures, a method for selecting seismic records based on the elasto-plastic dynamic amplification factor spectrum of base-isolated structures was proposed. The dynamic elasto-plastic time-history analysis method was first used to analyze the two degree of freedom simplified model of the base-isolated structure, and the dynamic amplification coefficient spectrum of the structure was obtained. Then, the seismic records were selected by the spectral matching method, and used to carry out the incremental dynamic analysis, seismic vulnerability analysis, and collapse capacity analysis of an 8-story base isolated structure. Finally, the two selection methods of seismic records were compared from the accuracy and discreteness of the analysis results. The results showed that the calculation accuracy of the proposed method for selecting seismic records is not much different from that of traditional methods, but it shows some advantages in reducing the discreteness of structural seismic response and the number of seismic records.