The layered soil model is used to simulate the nonlinear performances of the layered soil in this paper. Using the shear-displacement method, the flexibility coefficients of the pile-pile and the pile-soil are deduced based on the interaction mechanism of the pile-pile and the pile-soil in the layered soil. After that, the stiffness matrix of the pile-soil system can be established. Using coupling method presented in this paper, the interaction equation of superstructure-pile-raft-soil system is formulated. The interaction equations are used to analyze the reaction force on the pile head and the displacement characteristics of the raft of the piled-raft foundation in the layered soil and its practicality is excellent.