A coupled nonlinearly three-dimensional track-embankment-foundation numerical model for double line high-speed railway with a design speed of 350 km/h was established based on precisely modeling and multi-scale method. The material nonlinearities of foundation soil and embankment backfill were incorporated in the model. The infinite foundation was simulated using three-dimensional viscoelastic static-dynamic unified artificial boundaries. The dynamic reinforced concrete base-upper layer of formation interaction was modeled using dynamic algorithm. Considering the influence of static stress state prior to activation of moving loads on subsequent dynamic analysis, the generation of initial stress state of foundation and construction of embankment and track system were modeled based on multi-scale computation and element birth and death method; and then the movement of loads was simulated. The loads corresponding to the wheel set locations of CRH EMU train with 8 carriages were applied to the surface of the top layer element of rail. The attenuations of vibration acceleration spectra due to moving loads in track-embankment- foundation were summarized based on the calculated results.