Piled raft foundations can be effectively used when their hardness and bearing capacity are estimated sufficiently, and the total settlement, or the differential settlement, of the rafts, stays within a certain limit value. This research applies a 3D finite element method to analyze the response of the flat raft foundation when a minimum number of piles is installed under the raft foundation. The results show that when the pile length changes alternately (between the long pile and short pile), the settlement, the differential settlement, positive and negative moments, and the maximum shear force of the raft increase. The distance between the piles plays an important role in the performance of the piled raft foundation when the pile length is changed. It has a strong influence on the maximum settlement, differential settlement, bending moment of the raft, and distributes the load applied on the pile. In addition, the configuration of the piles is an important factor in the design of piled raft foundations. One reasonable pile configuration includes short piles being placed on the outside, and pile length being increased gradually from the outside to the center of the raft. The raft can also significantly influence the settlement between the center and the rim of the raft. When the thickness of the raft is increased to a certain value, the level of settlement is not significant. On the other hand, the raft's thickness has a small influence on the settlement of the piled raft foundation, it can affect the bending moment of the raft.