Abstract: Based on the indirect boundary element method (IBEM) with high precision, this paper solves the seismic response of a three-dimensional sedimentary basins both in the frequency domain and time domain. Taking the scattering of plane P and SV waves around an semi-ellipsoidal three-dimensional sedimentary basin as an example, the amplification effects of incident angle, wave type, incident frequency, length-width ratio and depth-width ratio of the basin on the ground motion are investigated in detail. The numerical results show that the basin shape has a significant impact on the amplification effect of seismic waves and the spatial distribution characteristics, and the detail effect also strongly depends on the frequency band of incident wave. In particular, as the basin depth increases, edge-generated surface waves become dominant, significant ground motion amplification effect can be observed for a wider band, and amplification area is mainly located in the middle of basin. The seismic wave focusing effect within the circular basin seems most significant, while that within long-narrow basin seems relatively weak, and multiple wave-focused areas appear within the basin for incident high-frequency waves. The amplification mechanism of basin effect on ground motion is different for different types of waves: for incident P waves, significant amplification of vertical displacement in the middle of basin can be mainly attributed to the focusing of surface waves generated from the basin edge; as for SV wave incidence, the surface wave focusing effect is relatively weak, but when the basin is deep, constructive interference of transmitted body waves and edge surface waves tend to result in a considerable amplification effect. For the wave-velocity ratio 1/2 between the alluvial basin and the bedrock, amplification factors of P and SV waves can reach up to 25, 15, respectively in frequency domain, and to 4.0, 3.7, respectively in time domain (Ricker waves). As for the low frequency waves, the displacement amplitude decreases from the basin center to basin edge, and the amplification is not obvious for the shallow basin. In addition, the angle of incidence also has significant impact on the amplitude and spatial distribution characteristics of ground motion.