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In this study, an effective model is proposed to predict the effect of nanoparticle agglomeration on the thermal conductivity of three-phase nanocomposites/polymers. In order to better describe this effect, the concept of agglomeration degree is introduced. The effect of particle volume fraction on thermal conductivity of composites is also studied by considering the interphase and agglomeration degree of particles. First, the relationship between agglomeration degree and particle volume fraction is discussed. Then, the effects of particle volume fraction, agglomeration degree and interphase thickness on thermal conductivity of composites are studied. The obtained results show that the agglomeration degree increases with increasing particle volume fraction. The thermal conductivity of composites increases first and then decreases with increasing particle agglomeration degree, and is also affected by the different thermal conductivity of particles and matrix, and the thickness of interphase.