Abstract: The superstructure analyzed by three-dimensional substructure method was divided into some substructures and the stiffness matrix be condensed from top to bottom.The boundary element method and the finite element method were applied to analyze the raft foundation on Winkler elastic foundation.The coupling equation was obtained by using both the equilibrium of force and the coordination of displacement.An engineering example was given to illustrate the method,and the results showed that efficiency and accuracy of the present method were higher than those of other methods.