In this paper, poly(glycolic acid–co-DL–lactic acid) (PGDLLA)/poly(ɛ-caprolactone) (PCL) incompatible nanocomposites were combined with multiscale modeling (MSM) in a ratio of 80/20. Since the behavior and mechanical properties of blends depend significantly on the interphase region, the compatibilizer poly(l,l-lactic acid–co-ɛ-caprolactone) (P(lLA-co-ɛ-CL)) was used to improve compatibility and graphene oxide (GO) was used to increase the interphase strength of PGDLLA matrix/PCL. This work was done by mixing solvent to achieve the optimum disperse of GO in the matrix. The investigation of interfacial phenomenon by the theoretical interfacial models is important. Under the assumption of constant modulus and elastic deformation in the zero interface region, the predictions in this region are more unreliable when the calculations of experimental mechanical properties are analyzed in detail. In this study, PGDLLA/P(lLA-co-ɛ-CL)/PCL compounds were compared with the MSM approach to predict the plastic deformation in the stress–strain behavior. In contrast to the hypothesis that a simple look at the interphase area in nanocomposites, a finite element code is proposed to evaluate the efficiency of the interphase area. Both experimental results and FEM analysis showed that Young’s modulus increases by incorporating GO into GO/PGDLLA/P(lLA-co-ɛ-CL)/PCL nanocomposites; the amount of increase for incorporating 1 phr GO is about 61%.