In this study, we investigated the effect of heterogeneity on the mechanical properties of epoxy resin by combining coarse-grained molecular dynamics (CG-MD) and finite element method (FEM) simulations. To evaluate the heterogeneity effect in the uniaxial elongation, heterogeneous and homogeneous FEM models of micrometer-scale cubic epoxy resin were constructed. For the heterogeneous FEM model, parameters of nanometer-scale elements were determined by CG-MD simulations, where nanometer-scale blocks have different cross-linked structures. For the homogeneous FEM model, the averaged parameters were used for all elements. The calculated stress-strain (S-S) curves of the heterogeneous model exhibit similar tensile stress values when compared to the experimental data, whereas the homogeneous model yields notably higher values. Moreover, a clear strain concentration associated with the formation of the shear band-like structure was observed in the heterogeneous model and not in the homogeneous model.