Ground vibrations generated by high-speed trains running along railways either at grade or on viaduct bridges, are greatly concerned by the railway industry. Considering the train-track-bridge-abutment-pile-soil interactions involved, modeling the problem in an analytical manner is almost impossible, while conventional numerical methods struggle to accurately simulate the dynamic properties of infinitely large soils. Therefore, this study introduces a new substructure methodology for train-track-bridge-abutment-pile-soil interactions that leverages an ingenious combination of the 2.5-dimensional finite element-boundary element method (2.5D FE-BE) for dynamics of infinitely long periodic structures, and a local 3-dimensional finite element model for pile-soil interaction. This innovative method allows for the consideration of detailed pile-soil coupling using a local finite element model, all while retaining the ability to account for the infinite size of the soil structure using the 2.5-dimensional finite element-boundary elements. After a comparison between model prediction and field measurement, the model is employed to explore the environmental vibration characteristics of on-viaduct high-speed railways and analyze the vibration reduction effects of various measures, including rail fasteners, track slab pads, and bridge bearings.