To validate the effect of FLAC^3D software on the seismic response analysis of soil, we used the No. 3 logging site (class Ⅱ site) in Xiangtang Town, Tangshan City as an experimental site and analyzed its seismic response using FLAC^3D software and an equivalent linearization method. The calculation results show that FLAC^3D software method is feasible. Then taking a class IV site in Tanggu District, Tianjin City as an example, the two methods are used to calculate the ground motion peak values and ground response spectra under different ground motion input intensities. The results show that the results calculated via FLAC^3D and the equivalent linearization method have little difference when the intensity of input ground motion is relatively small; moreover, FLAC^3D overcomes the problem of a long characteristic period of ground response spectrum when the input ground motion intensity is large. When using the equivalent linearization method, this problem occurs because of an underestimation in ground seismic response (high frequency) and an overestimation in soil nonlinearity. Therefore, the results obtained from the FLAC^3D method may be more appropriate for engineering practice.