An efficient domain decomposition method (DDM) is employed to improve upon the efficiency and capability of the finite element-boundary integral (FE-BI) method for calculation of electromagnetic (EM) scattering from deep cavities. This method first subdivides the original cavity into many sub-domains along its depth and classifies these sub-domains into a few building blocks. It then employs the substructuring method to deal with the different types of sub-domains. The resulting Schur complement system is solved by a special method which has low memory requirements because the formation of the global Schur complement matrix is not necessary. Numerical results indicate that the presented method is an effective approach for scattering by deep cavities.