The activation energies (E-J and E-J) calculated from the temperature dependence of the storage compliance (J) and the loss compliance (J) of carbon black (CB)-filled, hydrophobic silica- and hydrophilic silica-filled cross-linked natural rubbers (NRs) were found to be less than 15 kJ mol(-1), which corresponds to the physical range of van der Waals interaction. The results of three-dimensional-transmission electron microscopy measurements indicate that the closest distance (d(p)) between the two neighboring nanofiller aggregates centers decreased sharply with increasing nanofiller loading and tended to become constant at a nanofiller loading of around 30 phr or higher. For all samples examined, there were two regions related to the elastic deformation energy, and the critical d(p) value between the two regions was in the order of CB > hydrophobic silica = hydrophilic silica. Additionally, E-J developed in the region of longer d(p) than that of E-J. On the other hand, E-J occurred after the formation of the filler network and was larger than E-J. E-J is assumed to be related to slippage of the junction and the rearrangement of the nanofiller network. Therefore, the dependence of E-J and E-J on d(p) suggests that the interaction layer between the nanofiller and NR has at least two energy levels. (c) 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 2594-2602, 2013