A nonconformal twofold domain decomposition method (TDDM) based on the hybrid finite element method-boundary element method (FEM-BEM) is proposed for analyzing 3-D multiscale composite structures. The proposed TDDM starts by partitioning the composite object into a closed exterior boundary domain and an interior volume domain. The interior and exterior boundary value problems are coupled to each other through the Robin transmission conditions (RTCs). Both domains are then independently decomposed into subregions to facilitate computation. Specifically, FEM-DDM with the second order transmission conditions (SOTCs) is employed for the interior domain, and BEM-discontinuous Galerkin (BEM-DG) based on the combined field integral equation (CFIE) is applied for the exterior boundary domain. The proposed TDDM allows for nonconformal discretization between any touching subdomains. Without the introduction of a stabilization term that relies on a line integral over intersection of nonmatching meshes and relevant terms involving surface-line integrals, the proposed TDDM provides an effective domain decomposition (DD) preconditioner for the global system. Numerical examples are presented, and the comparisons of the simulation results with FEM-BEM confirm the validity and accuracy of TDDM. Moreover, its ability to model practical large-scale and multiscale targets is also demonstrated.