Aiming at the phenomenon of "disc settlement" that is common under the stiffness design conditions such as pile raft foundation, from the perspective of deformation control, the pile body at the bottom of the raft is regarded as a nonlinear spring, and the Q-s curve obtained from the single pile load test is used as the spring rate, and a simplified analysis model of pile raft foundation is established. Through numerical simulation, three design methods, planar variable stiffness, vertical variable stiffness and spatial variable stiffness, were used to reduce the differential settlement of raft foundation, and the settlement characteristics of various design methods under uniform load of pile raft foundation were compared and analyzed. The results show that the spatial stiffness of the pile raft foundation can effectively reduce the differential settlement of the foundation, improve the force deformation characteristics of the foundation, and reduce the amount of materials, and the technical and economic benefits are significant.