A coupled model of a track-layered ground-in-filled trench system is developed to investigate the isolation effects of an in-filled trench on reducing vibrations generated by moving train loads. By using the substructure method, the whole model is decomposed into two parts: the layered ground containing the in-filled trench and the track. Firstly, the flexibility coefficient for moving uniformly distributed loads applied on the layered ground containing the trench is obtained by using the 2.5D indirect boundary element method. Then, the dynamic equilibrium equation of the track under the moving train loads and uniformly distributed loads are established. Finally, the layered ground and the track are coupled according to the equivalence between the deformation of the track and the vertical displacement of the layered ground. The validity of the method is confirmed by comparing its results with the published ones. Numerical calculations are performed by embedding an in-filled trench in a homogenous ground, in a single layered ground and also in the real site at Ledsgard as examples. The results show that the isolation effects are different for different ground conditions and for different geometric parameters such as the depth, width and location of the in-filled trench.