Dynamic numerical simulation of pile-supported slab track system embedded in a soft soil and embankment was performed. 3D model was formulated in a time domain to consider the non-linearity of soil by utilizing FLAC 3D, which is a finite difference method program. Soil non-linearity was simulated by adopting the hysteric damping model and liner elements, which could consider soil-pile interface. The long period seismic loads, Hachinohe type strong motions, were applied for estimating seismic respose of the system, Parametric study was carried out by changing subsoil layer profile, embankment height and seismic loading conditions. The most of horizontal permanent displacement was initiated by slope failure. Increase of the embedded height and thickness of the soft soil layer leads increase of member forces of PHC piles; bending moment, and axial force. Finally, basic guidelines for designing pile-supported slab track system under seismic loading are recommended based on the analysis results.