Analysis of soil-structure interaction is commonly conducted by dividing the infinite domain of the soil into two domains: interior and exterior domains. The interior domain is bounded in a small region, while the exterior domain is replaced by artificial boundary conditions. The choice of artificial boundary conditions is a critical issue in the analysis of soil-structure interaction problems. Perfectly matched discrete layer (PMDL) has been proved as a good approach for modeling the exterior domain. In this study, a modified version of the PMDLs, i.e. PMDLs with analytical wavelengths (AW-PMDLs), is used in the soil-structure interaction analysis in time domain, which essentially can be regarded as an extension of the analysis in frequency domain, being previously proven to be effective. Numerical verifications are implemented. The results demonstrate that the proposed method performs well in the analysis of soil-structure interaction problems in time domain.