Embankment with pile-supported foundation (PSF) is widely used for high-speed railway (HSR) built in soft ground. Although extensive studies have been conducted on the effectiveness of PSF in reducing ground vibration via numerical analyses, the soil-water coupling in soft ground and response discrepancies among different types of PSF are seldom considered. In this study, 2D elastoplastic FEM was conducted to verify the necessity of soil-water coupling analysis and clarify the response discrepancies among different types of PSF, such as pile-net foundation, pile-raft foundation and pile-plate foundation. Numerical results indicate that liquid phase in soft ground plays an important influence on the dynamic response of HSR, the vertical acceleration and displacement will be overestimated while EPWP will be underestimated if soil-water coupling is not considered. Besides, single-phase analysis exaggerates the acceleration attenuation and underestimates the vibration amplification in soft ground. PSF induces significant stress fluctuation in the embankment and stronger vibration beneath the pile end compared to the unreinforced ground, moreover, the distributions of vertical acceleration and EPWP from PSF are partitioned sharply by the piles while vertical dynamic displacement becomes more uniform within the pile reinforced area. The peak acceleration and EPWP in soft ground are significantly different among different types of PSF, overall, the larger stiffness of PSF is, the smaller the peak acceleration and EPWP may be. However, the peak displacements are similar in different cases for the dynamic displacement is basically controlled by the piles rather than the slab or pile cap. The present research gives an insight to analyze high-speed train induced EPWP and settlement accumulation in soft ground.