This study investigates the pile foundation of a nuclear power plant situated on medium-soft soil. It employs an improved viscoelastic artificial boundary unit to accurately simulate the boundary conditions of the calculation area. The research utilizes a constitutive model of concrete damage plasticity for the pile foundation and an equivalent linearized model for the soil layer. Through large-scale shaking table experiments and numerical simulations, we explore the internal force distribution within the nuclear power structure’s pile foundation and assess the extent of the damage. The results indicate that damage primarily occurs in the medium-soft ground, concentrating in the upper part of the pile and affecting the entire cross-section. Subsequent numerical analyses were conducted after reinforcing the soil layer around the top of the pile. The findings demonstrate that this reinforcement leads to a more uniform and rational distribution of internal forces along the pile, significantly reducing damage. Notably, there is no severe damage extending across the entire cross-section after reinforcement. This outcome highlights the potential for improving the force distribution in the pile foundations of nuclear power structures through appropriate soil layer reinforcement. The insights gained from this study provide valuable guidance for the seismic design of nuclear power structures.