Rayleigh damping is proportional to the combination of the structural mass matrix and stiffness matrix and is widely used in structural seismic analysis. The accuracy of seismic analysis of nuclear power structures directly depends on the value of the Rayleigh damping parameters. However, the stiffness component of Rayleigh damping is not included in the explicit integral, so the Rayleigh damping in the explicit and implicit integrals needs to be handled differently. LS-DYNA R11.1.0 software provides various calculation methods for the value of the Rayleigh damping parameter in the explicit integral. To investigate the influence of the value of the Rayleigh damping parameter in the explicit and implicit integrals on the results of the dynamic analysis of a nuclear power plant, the AP1000 nuclear island plant is taken as an example, and the explicit and implicit dynamic calculation are carried out respectively for the nuclear power plant, considering the soil–structure interaction. The results show that the Rayleigh damping parameter calculated by different methods in the explicit integral has a large influence on the results of seismic analysis of nuclear power plants. The mass component of Rayleigh damping in the explicit and implicit integrals takes the same value, and the stiffness component of Rayleigh damping in the explicit integrals is taken as the negative of the stiffness component in the implicit integrals. Thus, the results of the two dynamic analyses can be in good agreement. The results provide a reference for the application of Rayleigh damping in the explicit integral for the seismic analysis of nuclear power structures.