In this paper, to evaluate the applicability of four equivalent linear analysis programs, i.e., SHAKE 2000, DEEPSOIL, EERA, and Strata, the bedrock seismic wave was chosen as the input motion on a deep site. The initial shear modulus was determined according to the shear wave velocity and density of the soils, and the corresponding modulus decay curves and damping ratio curves were assigned. Surface acceleration time-histories, the corresponding acceleration response spectra, and the Fourier amplitude spectra were obtained by using the four programs. In addition, the maximum shear strain and peak ground acceleration vs. depth for the site were plotted. The results showed that the acceleration response spectra and the Fourier amplitude spectra obtained by the four programs were identical. The plots of maximum shear strain and peak ground acceleration vs. depth obtained by program Strata were different from those of the other three programs due to different division of soil layers. The differences among the four programs were summarized as well. The dynamic properties of soil can be comprehensively considered using DEEPSOIL with more formulas, and the random vibration theory proposed by Strata could be used for equivalent linear analysis.