Thin-layered method (TLM) is very efficient to study the wave propagation in layered ground, and boundary element method (BEM) is very precise to solve infinite domain problems. This paper simplifies the track-ground substructure model, then combining the advantages of the above two methods, it presents 3D semi-analytical BEM based on TLM, on which the Green’s function is regarded as fundamental solution of a stratified half-space. Due to the vertical inhomogeneous ground, the effects of geometrical and material properties of the WIB were investigated in detail and the results show that increasing the shear modulus、thickness and width of WIB can improve the isolation effect under rail transit load. At the same time, relatively small embedment depth can give a satisfactory isolation effect．In addition, the foundation of the stratification parameter and the characteristics of non-uniform have a little influence on the vibration isolation effect of the WIB.