Tuned mass damper (TMD) has been applied in civil engineering fields to reduce the seismic response. However, few TMDs are used in the nuclear structure due to the huge additional mass of the traditional TMD device on the nuclear structure. In this paper, the PCS water tank of a nuclear structure is reconstructed into a TMD system to reduce the seismic response of the nuclear structure. The proposed novel water tank-TMD device can use its characteristics of large mass to achieve the tuned shock absorption effectively while maintaining the original function of the water tank. Moreover, more and more nuclear power structures are being built on non-bedrock sites, and the effects of soil-structure interaction (SSI) on the seismic response and seismic migration performance of nuclear power structures need to be reasonably considered. The effects of SSI and auxiliary plants on the seismic response of the nuclear containment plants equipped with PCS water tanks are first investigated. Subsequently, the performance of the water tank-TMD system in reducing the seismic responses of nuclear containment plants is analyzed in detail by considering the effect of SSI, design frequency of TMD, and design criteria of TMD. The research results show that the proposed water tank-TMD system can effectively reduce the seismic response of nuclear containment plants. Besides, it is necessary to consider the influence of SSI on the dynamic characteristics of the structure in the design of TMD when the SSI effect is strong. The water tank-TMD system designed according to the TMD criteria proposed by Sadek et al., and Salvi and Rizzi has better reduction performance compared with that designed by other design criteria.