The composite of epoxy polymers and a-alumina fillers is used as a heat dissipation material. The fillers often agglomerate with nanometer-depth polymers sandwiched in between. We address theoretically the effective thermal conductivity of such a filler-polymer-filler system. The non-equilibrium molecular dynamics simulation is performed to obtain the effective thermal conductivity of the system, in which bisphenol-A (bisA) epoxy polymer sub-system with depth 14-70 angstrom is inserted between two alpha-alumina slabs. Effects of surface-coupling (SC) agent are also investigated by adding model molecules to the polymer sub-system. For smaller polymer-depth cases, the effective thermal conductivity is determined essentially by the interfacial thermal conductance that relates to the temperature-gaps at the interfaces. We find for the interfacial thermal conductance that: (i) it is decreased by decreasing the polymer depth toward the chain length of a single bisA molecule, and (ii) it is increased by adding the SC molecules to the polymer sub-system. Combining separate simulation analyses, we show that the (i) results from effectively weakened interaction between a bisA molecule and two alpha-alumina slabs due to the orientation constraint on the bisA molecule by the slabs. Reasons of the (ii) are enhancement of the following three quantities by addition of the SC molecules: the phonon population of the bisA molecules at those frequencies corresponding to that of acoustic phonons of alpha-alumina, the phonon transmission coefficient from the alpha-alumina slab to the polymer sub-system for the transverse acoustic phonon, and the group velocity of the transverse acoustic phonon in the polymer sub-system. (C) 2015 Elsevier Ltd. All rights reserved.