This study used the results from 45 microtremor array measurements to construct a shallow shear wave velocity structure in the western plain of Taiwan. We constructed a complete 3D velocity model based on shallow and tomography models for our numerical simulation. There are three major subsurfaces, engineering bedrock (VS = 600 m s-1), Pliocene formation and Miocene formation, constituted in the shallow model. The constant velocity is given in each subsurface. We employed a 3D-FD (finite-differences) method to simulate seismic wave propagation in the western plain. The aim of this study was to perform a quantitative comparison of site amplifications and durations obtained from empirical data and numerical modelling in order to obtain the shallow substructure soil response. Modelling clearly revealed that the shallow substructure plays an important role in strong ground motion prediction using 3D simulation. The results show significant improvements in effective shaking duration and the peak ground velocity (PGV) distribution in terms of the accuracy achieved by our developed model. We recommend a high-resolution shallow substructure as an essential component in future seismic hazard analyses.