Influences on the ground motion simulations by soil amplification effects and multiple seismic wave interferences in the heterogeneous medium are investigated. Detailed velocity structure obtained from the microtremor array survey is adopted in the ground motion simulation. Analyses for amplification ratios of core samples of ten drill holes with 40 m deep in the sedimentary layers show that the soil amplification ratio influences nonlinearly the seismic ground motion. Based on the above analysis results, the ground motion in the heavily damaged zone in the Japanese Kobe earthquake of 1995 is simulated in a digital SH seismic wave model by using the pseudospectral method with the staggered grid RFFT differentiation (SGRFFTD). The simulated results suggest that the heterogeneous velocity structure results in a complicated distribution of the maximum amplitudes of acceleration waveforms with multiple peaks at the surface. Spatial distribution of the maximum amplitudes coincides well with that of collapse ratios of buildings in Kobe. The dual peaks of the collapse ratios away from the earthquake fault coincide well with the double peak amplitudes of simulated seismic acceleration waves also. The cause for the first peak amplitude of the ground motion is attributable to the interference of the secondary surface wave from the bedrock propagating horizontally along the surface sedimentary layer and the body wave from the basin bottom according to analyses of wave snapshots propagating in inhomogeneous structure of the Osaka group layers. The second peak amplitude of the ground motion may be attributive to the interference of the secondary surface wave from the tunneling waves in the shallow sediments and the body wave. It is important for the study on complicated distributions of earthquake damages to investigate influences on the ground motion by soil amplification effects and multiple seismic wave interferences due to the structure. Explorations of the structure to the bedrock are necessary for the urban mitigation disaster. Seismic wave simulations are valid for aseismatic study.