Previous research often relied on simplified models that assumed a rigid connection between the superstructure and raft foundation. These models disregarded the influence of superstructure stiffness on soil-foundation interaction, leading to inaccurate predictions of raft bending moments, pile loads, and settlement. This paper investigated the impact of superstructure stiffness for three different structural systems (framing, coring and shear wall systems) on the behavior of piled raft foundation as well as the presence impact of a 2-meter sand replacement beneath the raft under various loads. A 3D nonlinear finite element analysis using PLAXIS 3D and ETABS was conducted in soft to medium clay overlying a dense sand layer. Incorporating the superstructure stiffness reduced the maximum raft bending moments by (6.6% to 9.1%), (39.0% to 47.9%), and (18.2% to 22.3%) as well as the maximum raft shear forces by (39.2% to 46.9%), (25.6% to 49.2%), and (34.7% to 44.9%) for framing, coring and shear wall systems ,respectively, under gravity, wind, and seismic loads. The presence of a 2m replacement layer beneath the raft had a negligible effect on the system's behavior(Less than 1.6%). In conclusion, the variation of superstructure stiffness affected the raft's internal forces; therefore, it can be economically advantageous to consider this while designing piled raft foundation.