A novel three-dimensional (3D) coupled train-track-soil interaction model is developed based on the multi-body simulation (MBS) principle and finite element modeling (FEM) theory using LS-DYNA. The novel model is capable of determining the highspeed effects of trains on track and foundation. The soils in this model are treated as saturated media. The wheel-rail dynamic interactions under the track irregularity are developed based on the Hertz contact theory. This model was validated by comparing its numerical results with experimental results obtained from field measurements and a good agreement was established. The one-layered saturated soil model is firstly developed to investigate the vibration responses of pore water pressures, effective and total stresses, and displacements of soils under different train speeds and soil moduli. The multi-layered soils with and without piles are then developed to highlight the influences of multi-layered soils and piles on the ground vibration responses. The effects of water on the train-track dynamic interactions are also presented. The original insight from this study provides a new and better understanding into saturated ground vibration responses in high-speed railway systems using slab tracks in practice. This insight will help track engineers to inspect, maintain, and improve soil conditions effectively, resulting in a seamless railway operation.