The connection between the structures and the linear viscoelasticity was revealed in this work for polymer nanocomposites containing agglomerated particles. A new image analysis method using the greyscale histogram of TEM images was suggested to determine the local volume fraction of nanoparticles inside an agglomerate, which represents the degree of agglomeration. It is found that the local volume fraction of nanoparticles is strongly related to the particle-polymer interaction. Such result was justified by a new rheological analysis based on the recently suggested modulus decomposition in the linear viscoelastic properties of polymer nanocomposites, from which the combined shift factor due to the hydrodynamic effect was used to quantify the local volume fraction of nanoparticles. Moreover, a two phase model was suggested to describe the linear viscoelasticity of such polymer nanocomposites. The success of this model in different polymer nanocomposites implies the rationality to regard the isolated agglomerate as a composite droplet in the polymer matrix. (C) 2016 Elsevier Ltd. All rights reserved.