Numerical modeling of electromagnetic problems becomes very challenging when large systems with complex structures need to be designed. This paper proposes a novel second-order transmission condition (SOTC) for the non-conformal finite element domain decomposition method (NC-FEM-DDM), which can be implemented efficiently on non-conformal interfaces via a Gaussian integration. The proposed SOTC is then compared with several existing transmission conditions (TCs) employed in DDM. The results show that the SOTC derived in this paper has a more clustered eigenvalue distribution and hence a better iterative convergence. Numerical results of real-life applications both in high and low frequency bands further demonstrate the efficiency and capability of this SOTC for modeling computationally challenging problems.