Abstract: In order to obtain the seismic wave of the bedrock in a thick soft soil site, the inversion program based on wave propagation theory and equivalent linearization technique is developed. Six bedrock acceleration time histories under typical Shanghai soft soil are inverted by a self-compiled inversion program, and they are validated by the comparison with forwarded simulation. Then, the finite element model of the subway station considering soil-structure dynamic interaction is established, and the bedrock time history inverted El-Centro wave is selected as input motion to conduct the dynamic response analysis of an underground structure in a soft soil site. The analysis results show that: the seismic wave inversion program can attain the precise inverted bedrock motions; for different types of seismic waves, the ratios of peak surface acceleration to bedrock acceleration are significantly different; compared to superstructures, an underground structure has a larger horizontal displacement, but the relative horizontal displacement between top and bottom plates is small.