Abstract: Soil-structure interaction analysis is an important step in seismic design and safety assessment of nuclear power structures. Material damping and non-linearity are important factors affecting the structural response in the analysis of soil-structure dynamic interaction of nuclear power structures. If the frequency-domain method is used, the damping can be easily considered, but the equivalent linearization is needed to consider the non-linearity, which is not suitable for strong earthquakes, The time-step integration method is suitable for considering non-linearity, but Rayleigh damping model is generally used for material damping. Except for a few modes with specified damping ratio, the response of other modes will be restrained by the large damping determined by Rayleigh damping model, which makes the seismic response quite different from the real situation. If the modal superposition method is used, the damping effect can be reasonably taken into account, but the non-linearity can not be taken into account in the modal superposition method. Therefore, how to reasonably consider the damping and non-linearity is an important issue in the soil-structure interaction analysis of nuclear power structures. Considering that the main structure of nuclear power plant is rigid, and it is not easy to enter the non-linearity under earthquake, a new method for soil-structure interaction analysis is proposed in this paper. The modal superposition method is used to structure analysis, and the soil and foundation is analyzed by the explicit time-step integration method, the influence of infinite domain (radiation damping) is considered through artificial boundary conditions. This partitioned algorithm of soil-structure interaction based on modal superposition and time-step integration is realized, and verified by a simple example. Then, the soil-structure interaction analysis of a CAP1400 nuclear power structure is conducted, with the modal damping and Rayleigh damping are adopted respectively. The difference between modal damping and Rayleigh damping on the structure and site response is compared and analyzed. The results show that the structural damping model has little effect on the site response, but has obvious effect on the structure response.