A multiscale homogenization analysis is performed on polymeric nanocomposites containing clustered nanoparticles, based on which it is identified that the clusters cause the degradation of the elastic properties of the polymeric nanocomposites. The percolated interphase zone near the clustered nanoparticles is characterized by molecular dynamics simulations and finite element homogenization analyses. The elicited elasticity changes are attributed to the increases in the radius of the effective cluster when the embedded nanoparticles are closely packed. It is concluded that the equivalent cluster-based homogenization approach can provide high-computational efficiency without loss in accuracy.