The degradation mechanism of mechanical properties of a polymer nanocomposite consisting of agglomerating fillers is elucidated. It is found that overall elastic moduli of nanocomposites obtained through molecular dynamics simulation decreases according to agglomeration of the two embedded nanoparticles, which prevent efficient formation of interphase zone. Meanwhile, no prominent local field fluctuation by the agglomeration is observed. A percolation-related interphase model based on multiscale mathematical homogenization method is thus proposed to describe the degradation of nanocomposites in terms of the properties and overlap of interphase zone. Extensibility of the proposed model to a polydisperse nanoparticulate composites model is also confirmed. (C) 2015 Elsevier B.V. All rights reserved.