In the present study seismic wave propagation in heterogeneous media is numerically simulated by using the pseudospectral method with the staggered grid RFFT differentiation in order to clarify the cause for the complicated distribution characteristics of strong ground motion in regions with basin structure. The results show that the maximum amplitudes of simulated ground acceleration waveforms are closely related to the basin structure. Interference of seismic waves in the basin strongly affects the distribution of maximum seismic waveforms, which may result in peak disasters during earthquakes. Peak disasters might be away from basin boundaries or earthquake faults. Seismic energy transmitted into the basin from the bedrock can hardly penetrate the bottom of the basin and then travel back into the bedrock region. The seismic energy is absorbed by basin media, and transferred into the kinematical energy of seismic waves with great amplitude in the basin. Seismic waves between basins may result in serious damage to buildings over the basin. This is significant for aseismatic research. Geological surveys in and around urban areas would benefit aseismatic research and mitigation of seismic disasters of a city. Such geological surveys should involve seismic velocity structure in the media above the bedrock besides such subjects as active faults and geological structure.