In the seismic response analysis of locally irregular sites such as basins under plane wave incidence, it is usually assumed that the input seismic motion is of a single wave type, i.e., SV wave, SH wave, or P wave. However, the actual incident motion is generally a multi-dimensional coupled shaking case. Based on the spectral element method, the ground motion response of a three-dimensional semi-ellipsoidal sedimentary basin under the vertical incidence of plane waves is simulated. By analyzing the distributions of peak ground acceleration (PGA) and the corresponding amplification factor, the seismograms along the surface point profile, and the response spectrum ratio distribution at the characteristic frequencies, the ground motion amplification features of the sedimentary basin under multi-dimensional ground motion input are investigated through comparisons with the results of single wave type incidence. The results show that compared with the unidirectional horizontal seismic excitation, the bidirectional horizontal seismic input has a significant amplification effect on ground motion in the basin, and the maximum amplification factor can reach 1.87. Considering the influence of simultaneous input of bidirectional horizontal ground motion, the distribution characteristics of the peak ground acceleration will change significantly. The superposition and interference of waves propagating in different directions result in an asymmetrical PGA distributions. The bidirectional ground motion input makes the wave propagation characteristics more complex, and the location of the strongest ground shaking changes. In addition to the amplification of the response spectrum value, the bidirectional input also has a certain influence on the distribution of the predominant period.