Nanofluids have been proposed to have superior heat transfer ability than typical coolant, but the mechanisms of thermal conductivity enhancement still remain obsecure. This study, by using Molecular Dynamics simulation, specifically investigate the aggregation effect in nanofluids system. Non-Equilibrium Molecular Dynamics (NEMD) method is used to calculate the thermal conductivity of nanofluids system containing aggregated nanoparticles. The clustering phenomena is characterized and a simple model is proposed to explain the results qualitatively. Also the thermal properties of several nanofluids system consist of different shapes of aggregation are examined. A resistance-analogy model is found to explain the thermal transfer behavior between two limiting conditions.