In the process of structural dynamic time-history analysis, reasonable ground motion selection is always a difficult point in engineering. By improving the existing harmony search method for ground motion selection, dynamic time-history analysis is performed for two differently periodic prestressed concrete (PC) frame structures designed according to currently Chinese codes. Then, it is compared with the periodic point method, the dual-band method and the area method for calculation results. The results show that the discreteness of structural response parameters of the periodic point method and the improved harmony search method is smaller in frequently earthquake, and the coefficient of variation is about 10%. Compared with the base shear force of mode-superposition response spectrum method, the dual-band method and the improved harmony search method are more in accordance with the standard design. Structural response parameters of the area method and the improved harmony search method are smaller dispersion in rarely earthquake, and the coefficient of variation is about 15%. Furthermore, the results of the periodic point method are the most dispersion. The periodic point method is only applicable to the ground motion selection process of elastic time-history analysis. The improved harmony search method is applicable to both elastic and elastic-plastic time-history analysis, which can meet standard design and engineering requirement.