Piled raft foundation is gaining popularity as a composite foundation system economizing foundation design for tall, heavy structures. The seismic response of a piled raft foundation would involve complex raft–soil–pile interaction as well as pile–soil–pile interaction, which cannot be estimated efficiently by existing methods available for pile groups. This paper discusses the development of a numerical model to study the seismic response of piled raft foundation system by substructure method-based seismic soil-structure interaction (SSSI) analysis using SASSI 2010 program. The flexible volume substructure method is used to analyze SSSI problem. Published data from a centrifuge test to study earthquake response of a piled raft system in soft clay was selected for the simulation. Results from the analysis are compared with experimental data. © Springer Nature Singapore Pte Ltd 2019.