Abstract: A wave free-field calculation method suitable for non-equidistant spectral element nodes under vertical and oblique plane wave incidences is developed based on the transfer matrix method. On this basis, the wave scattering problems in locally saturated fields under plane wave incidences are simulated by combining high-precision spectral element method and multi-transmitting formula. Based on this method, the ground motion characteristics of the Kitimat basin in Canada under vertically incident SV waves are investigated considering the near surface saturated soil layers. By comparing the results with those of linear elastic sedimentary basins, the influence of saturated soil layers on the amplification effect of ground motion in two-dimensional basins with complex basement geometries and layered soil layers is analyzed. The results show that the method proposed in this paper has high accuracy in simulating the seismic motion of locally saturated sites. When considering saturated soil layers, the surface seismic motion of the basin is enhanced, with the maximum amplification factor of about 1.08 and 1.8 for horizontal and vertical component displacements, respectively. However, the distribution features of seismic peak values are similar to those of single-phase medium basins. The dispersion phenomenon of surface waves is more significant in saturated basins, with longer shaking duration and resulting in stronger constructive interference between different seismic phases. Some sites exhibit dominant frequency shifts, and the amplification characteristics in the frequency domain also show significant changes. The position of the maximum discrepancy corresponding to different frequencies has a good correlation with the thickness of the soil layer. As the porosity increases, the amplitude of surface displacement increases, and the formation and propagation of surface waves are also affected.