Previous studies on seismic demand analysis of pile-pier systems of bridge structures primarily focused on unidirectional ground motion, frequently overlooking the multidirectional nature of earthquake forces. Furthermore, research on the effects of soil-foundation-superstructure interaction on nonlinear soil and structure behavior in the context of bidirectional seismic motions is limited. This study addresses these gaps by assessing the seismic behavior of a pile-pier system of a high-speed rail (HSR) viaduct using three-dimensional nonlinear finite element analysis. The study examines eight near-field and eight far-field earthquakes using a comprehensive approach that considers earthquake scaling and nonlinear soil-structure interaction. The pier is represented as a three-dimensional solid element, while the viaduct is represented as a lumped mass attached to the top of the pier. A pile group embedded in clay supports the pier and viaduct. The current numerical model uses a hardening soil model with small strain stiffness for the soil and an elastoplastic model for the concrete material. A real-time history of seismic motion is used, which includes both unidirectional and bidirectional seismic analyses. In the pile-pier system, critical response parameters such as bending moment and shear force are compared. Finally, design implications are suggested.