In existing dynamic elasto-plastic analysis of supertall structures, rigid foundation assumptions are commonly adopted, neglecting the influence of soil-structure interaction. To investigate the effects of soil-structure interaction on supertall structures, a refined three-dimensional nonlinear finite element model of soil-foundation-superstructure was established and dynamic elastoplastic analysis of a 366m supertall tower in case of rare earthquakes was conducted. A one-dimensional equivalent linearization analysis based on the engineering site conditions was first conducted to capture the seismic response of the soil layers. Subsequently, the wave propagation method was utilized to resolve seismic wave input issues in the three-dimensional soil layers and then the accuracy of the adopted approach was validated. The results indicate that the natural period of the tower increases compared with the rigid foundation assumption when considering soil-structure interaction. Under the estimated rare seismic action, considering soil-structure interaction leads to a reduction in the overall seismic response of the tower. The inter-story drift angles of the tower increase in the lower zone and decrease in the higher zone, with the maximum inter-story drift angle in the higher zone decreasing, exhibiting a trend that the deformation transfers to the bottom. The damage to the walls in the higher zone of the tower is alleviated, and the overall degree of stiffness degradation in the structure is reduced. Additionally, the base shear and overturning moments decrease when soil-structure interaction is considered. Individual locations of the tower’s mega-columns experience increased internal forces, highlighting the potential risk of neglecting the effects of soil-structure interaction. The proposed method comprehensively considers the influence of site soil, providing a more realistic simulation of the seismic response of supertall structures. © 2024 Science Press. All rights reserved.