A numerical study on the kinematic responses of pile-raft foundation subjected to vertically propagating S-wave seismic excitation was presented. The dynamic soil-pile-raft interaction was modeled by using the thin layered element method and the finite element method. The effective input motions of pile-raft foundation were expressed with dimensionless horizontal response factor IH and rocking response factor IR, which were the ratios of raft motions to free-field soil surface motion. The horizontal and rocking response factors of pile-raft foundation were compared with those of pile group and raft foundation. The effects of pile lengths, spacings and rigidities on kinematic response factors of pile-raft foundation were also studied. The results have shown that the neglect of the effect of the raft can result in too small an evaluation of the kinematic response factors of pile-raft foundation when the pile spacing is relatively large.