Using equivalent elastic-perfectly-plastic and hyperbolic-hysteretic constitutive models to respectively depict the dynamic behaviors of pile-pier systems and soft clay，a series of three dimensional（3D）explicit dynamic finite element analyses are performed，with the investigation foci placed on the acceleration amplification coefficients at different locations，and bending moments of both pile and pier during the seismic ground motions. Several important factors are considered，namely the peak bedrock acceleration（PBA），peak bedrock velocity（PBV），pile flexural rigidity，and bridge girder mass. It is found that the soft clay has significant amplification effect on seismic ground motion for PBA less than 0.15g；for PBA larger than 0.2g，the acceleration amplification coefficients are generally less than 1，indicating that significant hysteresis damping of clay is introduced during strong ground motions. The bridge girder mass is found to have an evident weakening effect on the acceleration response at pier top. On the other hand，largely due to the highly nonlinear behavior of clay under dynamic loading and the complex seismic clay-pile interaction，the increasing trends of maximum pile or pier bending moments against PBV are also significantly nonlinear；for PBV larger than 0.2m/s，plastic deformation of pile-pier system became significant；the pile flexural rigidity and bridge girder mass are found to have respectively more pronounced effects on the maximum bending moment responses of pile and pier，suggesting that their seismic responses are more dependent on the kinematic and inertial forces，respectively.