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As a transportation hub connecting sea and land, the seismic safety of an undersea tunnel is very important. Based on the structural and stress characteristics of a shield tunnel, a seismic response analysis of a coastal nuclear power plant under a complex foundation is carried out in this paper. Firstly, adopting the lateral and longitudinal response displacement methods, the authors study the variation and distribution features of the rate of diameter change and joint-stretching value of the shield tunnel segments. On this basis, a three-dimensional refined finite element model of a sinking tube–soil mass under a complex soil foundation is established. Finally, when the joints and segments of the shield tunnel are subjected to ground motion, the deformation and internal force distribution of its lining segments are studied. The findings show that under influence of SL-2-magnitude ground motion, the soft–hard stratum junction is the weak point of the shield tunnel structure’s longitudinal seismic resistance. When the silt layer at the position of the shield segment is thicker and the geological conditions are relatively poorer, the internal force, diameter deformation rate, and joint-stretching value will be larger. The research results can provide a reference for seismic research on shield tunnels in sea areas under complex foundations.