Abstract: The seismic safety of nuclear islands constructed in loose and soft deposits subjected to strong earthquake motions is becoming a major engineering challenge. An example of such nuclear islands is the AP1000 nuclear islands located in the coastal deposits, China. Using the three-dimensional (3D) finite element method, we conducted a nonlinear seismic response analysis of a pile-raft-supported AP1000 nuclear island building. In the proposed response analysis, the engineering geology characteristics and nonlinear dynamic behavior of the soils, the artificial boundary conditions and the simulation model were considered in detail. A special emphasis was given to the 3D model for the pile-raft-supported AP1000 nuclear island building and the input bedrock motions from the near-field, middle-far-field, and far-field strong earthquakes. The spectral accelerations (SAs) of the nuclear island building were more intense to the bedrock motion frequency components close to the fundamental frequency of the main structure of the nuclear island. The SA predominant periods were almost the same as those of the bedrock motions. The influence of the seismic responses of the sloshing water in the water storage tank (cooling system) on the nuclear island building was similar to the whipping effect. The peak acceleration amplification factors (PAAFs) increased with the increasing nuclear island heights. The PAAFs were mainly dependent on the nuclear island itself and the seismic wave propagating from bedrock to nuclear island base through soft deposits for the near-field and far-field strong earthquake motions, respectively. The peak relative displacements (PRDs) between the various nuclear island heights and its base increased with the increasing heights, and the PRDs to the far-field strong earthquake motion ware more intense. With the increasing peak bedrock accelerations, the PAAFs of the nuclear island building were decreased while the PRDs were increased. The flexible ground and the soil-pile-raft-nuclear island building interaction had an effect on the high-frequency de-amplification and the low-frequency amplification for the bedrock motions. It significantly increased the peak acceleration at the lower part and decreased it at the middle-upper part of nuclear island building.