Metal nanoparticle has been a promising option for fillers in thermal interface materials due to its low cost and ease of fabrication. However, nanoparticle aggregation effect is not well understood because of its complexity. Theoretical models, like effective medium approximation model, barely cover aggregation effect. In this work, we have fabricated nickel–epoxy nanocomposites and observed higher thermal conductivity than effective medium theory predicts. Smaller particles are also found to show higher thermal conductivity, contrary to classical models indicate. A two-level effective medium approximation (EMA) model is developed to account for aggregation effect and to explain the size-dependent enhancement of thermal conductivity by introducing local concentration in aggregation structures.