Abstract: The influence of nanoparticle-polymer interaction on aggregation process of nanocomposites was studied by molecular dynamics simulation using coarse grained model. Results show that the cluster structure of system during aggregation is determined by the interaction, and a higher interaction leads to a higher fractal dimension of cluster. The fractal dimension of system with interaction strength between particles εNP=1.0 is 2.05, in consistent with TEM picture of polyimide-carbon black composites system. Result of simulation on dynamic percolation system shows the higher interaction leads to a delayed percolation time and a decreased percolation transition rate, which agrees well with experimental observation in dynamic electrical percolation.