In this paper, a multi-transmitting formula (MTF) was integrated into ANSYS software through secondary development, enabling dynamic finite element simulation of wave propagation in infinite domains. The numerical reliability and accuracy of the MTF were verified through a plane wave problem involving a homogeneous elastic half-space, as well as 3D scattering and source problems in a three-layered soil site. Additionally, a comparative analysis of various artificial boundaries was conducted to highlight the advantages of the MTF. Field observations of environmental vibrations caused by high-speed railway operations revealed localized amplification of vibrations along the depth direction at the Kunshan segment of the Beijing–Shanghai high-speed railway. Based on these observations, a series of numerical analyses were conducted using the customized ANSYS integrated with the MTF to investigate the underlying causes and mechanisms of this phenomenon, as well as the spatial variation characteristics of foundation vibrations induced by bridge vibrations during high-speed train operations. This study reveals the mechanism by which the combined effect of bridge piles and soft soil layers influences the depth variation in peak ground accelerations during site vibrations. It also demonstrates that the presence of bridge piers and pile foundations effectively reduces vibration intensity in the vicinity of the railway, playing a crucial role in mitigating vibrations induced by high-speed train operations.