A semi-analytical procedure for determining the dynamic flexibility coefficient of the three-dimensional viscoelastic non-homogeneous foundation is developed. In this method, the foundation is divided into a number of layers and the displacement functions are expressed as the product of spline function and Fourier's series. The non-homogeneity of soil modulus along depth is taken into account. Then the flexibility coefficients can be obtained by solving the Lagrange's equation. The discussions cover both the horizontal and the vertical response. The results obtained are compared with the results obtained by other methods. It may be considered as an applicable method for the interaction analysis of structure-foundation system.