Abstract: Pile foundations have been widely adopted in civil engineering, but they have not been extensively applied in seismic category I nuclear structures. A coastal nuclear power plant uses pile foundations for its water intake structure, which lies in the transition zone of backfill soil and bedrock with inclined interfaces. Soil-pile interaction, the selection of artificial boundaries, and the simulation of hydrodynamic pressure are major technical difficulties. By building a three-dimensional refined finite element model of the entire soil-structure-pile system and using time-domain analysis with viscoelastic artificial boundaries, and the Housner spring-mass model is used to characterize hydrodynamic pressure inside the channel. Axial forces, shear forces, bending moments, and displacement responses under different working conditions were collected to evaluate the seismic performance of the pile foundation. This method can guide the design and seismic assessment of similar water intake structures in coastal nuclear power plants.