Thermal interface materials have been widely adopted in the thermal management for electronics system. Most of the thermal interface materials are made of polymers with thermally conductive particles distributed inside to enhance the thermal conductivity. Thus it is essential to figure out the effective thermal conductivity of this composite material. In the present paper, a parameterized cubic cell model had been developed and implemented by the finite element method. The numerical simulations were carried out to investigate the effect of the filler distributions on the effective thermal conductivity of the thermal interface materials. The volume percentage loadings of the particles ranging from 13% to 74% had been considered, and different particle distribution patterns had also been analyzed. The simulation results were compared with the experimental data as well as other models. A fairly good agreement was obtained for the particle volume percentage loading under consideration, which verified the developed cubic cell model.