To improve the accuracy of artificial boundary settings in soil-structure systems, this paper investigates lateral artificial boundary issues in three-dimensional soil-structure interaction systems based on the Finite Particle Method (FPM). First, the effects of lateral and longitudinal boundaries under different damping ratios are analyzed for a single-layer homogeneous site model. The boundary settings for a layered homogeneous site model are then explored, and the influence of these boundary conditions on the seismic response of the superstructure is evaluated. The results show that, compared to free and fixed boundaries, sliding boundaries effectively reduce the reflection errors caused by seismic waves passing through artificial boundaries, allowing for the simulation of a semi-infinite soil domain. For three-dimensional soil-structure systems, setting the distance from the soil boundary to the structure boundary equal to the thickness of the soil layer provides sufficient computational accuracy. This study offers a novel method for boundary settings in complex soil-structure seismic response analysis while reducing computational costs.