A multiscale homogenization analysis is performed on polymeric nanocomposites containing nanoparticulate clusters. Information obtained from molecular dynamics simulations is up-scaled to the continuum mechanics level to investigate the effect of agglomeration of spherical silicon carbide nanoparticles on mechanical behaviors of nanocomposites based polypropylene matrix. According to interphase percolation model characterized by molecular dynamics simulations and finite element homogenization analysis, the degradation of elastic properties of interphase zone near the clustered nanoparticles is applied to observe the elastic behavior of polymeric nanocomposites for various state of nanoparticulate agglomeration. Additionally, new index clustering density is proposed by the parametric studies to identify factors which mainly affect the mechanical properties of nanocomposites. The newly defined index represents the degree of nanoparticulate agglomeration in unit cells. Through homogenization results in case of the various nanoparticulate agglomeration, the correlation between the clustering density and the mechanical behaviors of nanocomposites is understood. It is possible that the homogenized elastic modulus of nanocomposites is predicted by the clustering density concept without large error. This approach is extended to different nanoparticle’s volume fraction cases. It is investigated that nanocomposites stiffness decrease from 10 to 30 % as the clustering density increases.