The finite-difference analysis WEAPR-S2 (Hung, 2020) for piled raft foundation has the disadvantage to provide the information of pile loads and pile stiffness owing to its discrete nature. To understand better the loading mechanism of such foundation, this study is aimed to investigate the responses of piled raft foundation using the three-dimensional finite element analysis. Midas GTS-NX program is adopted for the FE analyses conducted in this study. Square piled rafts varying with the width of raft and the ratio of pile spacing distance to pile diameter (S/d) were assumed locating at the ground surface of homogeneous clays. Mohr-Coulomb model was used to model the undrained soils. Vertical uniform loads were applied on top of the raft. The foundation settlements, pile loads, equivalent pile stiffness and the corresponding reduction ratios of the pile stiffness were monitored. It is found that: Shear wave velocity (Vs) of the soil will affect the foundation settlements significantly. The foundation settlements are larger at the center and become smaller at the corner. 2. The foundation settlements are also affected by the ratio of S/d. As the ratio of S/d increases, the settlements become larger. Their influences become smaller when soils become much stiffer. 3. The total load carried by the piles will become less when the soil becomes stiffer. The load carried by the single pile will increase as the S/d ratio increases, however the total pile load would drop. The pile load distribution will be strongly affected by the relative rigidity of the raft, for relative flexible raft, the center pile will carry the largest load among the piles, however as the raft becomes much stiffer, the load carried by the corner piles will become the largest. 4. As the relative rigidity of the raft becomes smaller, the importance of soil reactions is increased. Therefore the design of a group pile foundation and a piled raft foundation should be entirely different. 5. The equivalent pile stiffness is strongly affected by the soil stiffness. For rigid foundation, the pile stiffness will be larger at the center pile and smaller at the corner pile. However when more piles were installed in soft soils, the corner piles would exert the highest pile stiffness. The pile-to-pile interaction (PPI) is the reason to cause such phenomenon. 6. The effects of PPI are found different in flexible raft and rigid raft foundations. For flexible raft, the reduction of pile stiffness is found more significant at the corner piles, the reduced pile stiffness can be 30% of its original value. For more rigid raft, the reduction of pile stiffness due to PPI will be more significant at center of the foundation. The reduced pile stiffness can be 10% of its original value.