Under different foundation conditions, the floor response spectrum of nuclear island buildings exhibits varying characteristics. In the case of non-bedrock sites, the stiffness difference between the upper structure of the nuclear island buildings and the foundation becomes more pronounced, and the soil-structure interaction becomes more significant. Taking a nuclear island plant as a case study, the influence of different foundation conditions on the floor response spectrum of nuclear island buildings was investigated. A three-dimensional finite element model of the nuclear island buildings was established, and a massless foundation model was used to consider the soil-structure interaction. The floor response spectra of the nuclear island buildings under different foundation conditions were calculated and compared for analysis. The results indicate that soil-structure interaction must be considered when calculating the floor response spectrum of nuclear island buildings; as the site becomes softer, that is, as the shear wave velocity decreases, the peak frequency corresponding to the peak acceleration in the response spectrum curve shifts to lower frequencies, and the entire response spectrum curve exhibits a “leftward shift”; furthermore, as the shear wave velocity decreases, the peak acceleration of the floor response spectrum is amplified under certain shear wave velocity conditions, with the amplification effect being more pronounced in the vertical direction.