In this study, multiscale homogenization modeling to characterize the thermal conductivity of polymer nanocomposites is proposed to account for the Kapitza thermal resistance at the interface and the polymer immobilized interphase. Molecular dynamics simulations revealed that the thermal conductivity dependent on the embedded particle size originated from the structurally altered interphase zone of surrounding matrix polymer in the vicinity of nanoparticles, and clearly indicate strong dominance of interfacial phonon scattering and dispersion. To account for both the thermal resistance and the immobilized interphase, a four-phase equivalent continuum model composed of spherical nanoparticles, Kapitza thermal interface, effective interphase, and bulk matrix phase is introduced in a finite element-based homogenization method. From the given thermal conductivity of the nanocomposites obtained from MD simulations, the thermal conductivity of the interphase is inversely and numerically obtained. Compared with the micromechanics-based multiscale model, the thermal conductivity of the interphase can be obtained more accurately from the proposed homogenization method. Using the thermal conductivity of the interphase, the random distribution and radius of nanoparticles to describe real nanocomposite microstructure are considered, and the results confirm the applicability of the proposed multiscale homogenization model for further stochastic approaches to account for geometric uncertainties in nanocomposites.(C) 2013 Published by Elsevier Ltd.