Considering the dynamic nonlinear characteristics of soil by equivalent linear method, one-dimensional wave models were established to study the seismic effects along depth of deep soft sites under far-field ground motions of great earthquake. The results show that the magnified effect of acceleration response spectrum of each layer present more outstanding under far-field ground motions than under Suzhou artificial waves, with the increasing of bedrock peak ground acceleration, there is probability that the peak of long-period component of acceleration response spectrum appears higher than that of the short-period within 15m depth, which may adversely affect the long-period building structures. However, the reduction coefficient of peak ground acceleration (PGA) along depth according to the three levels of earthquake fortification standard was relatively higher when inputting far-field ground motions of great earthquake. As the curve fitted by Longjun Xu et al. based on records collected California Strong Motion Instrumentation Program geotechnical arrays of the United States and Hosokura Mine arrays of Japan, is not suitable for Suzhou area, suited quantitative formula about reduction coefficient curve of PGA with depth in deep soft site is given. Besides, maximum shear strain at the depth of approximately 15m and 40m present to be greatly changed when inputting far-field ground motions of great earthquake, with the growth of inputting bedrock peak ground acceleration, the layer in the depth of about 15m comes to be the most unfavorable position of shear deformation.