In this work, we proposed a spectral integral method (SIM)-spectral element method (SEM)- finite element method (FEM) domain decomposition method (DDM) for solving inhomogeneous multi-scale problems. The proposed SIM-SEM-FEM domain decomposition algorithm can efficiently handle problems with multi-scale structures, by using FEM to model electrically small sub-domains and using SEM to model electrically large and smooth sub-domains. The SIM is utilized as an efficient boundary condition. This combination can reduce the total number of elements used in solving multi-scale problems, thus it is more efficient than conventional FEM or conventional FEM domain decomposition method. Another merit of the proposed method is that it is capable of handling arbitrary non-conforming elements. Both geometry modeling and mesh generation are totally independent for different sub-domains, thus the geometry modeling and mesh generation are highly flexible for the proposed SEM-FEM domain decomposition method. As a result, the proposed SIM-SEM-FEM DDM algorithm is very suitable for solving inhomogeneous multi-scale problems.