Polymer materials stand on a very significant position in the materials industry area. The presence of organoclay nanocomposites reinforces polymer materials on many properties like strength, tensile and so on. Most previous studies on the characteristics of organoclays and polymer nanocomposites were based on the experimental approaches such as XRD (X-ray Diffraction) and NMR (Nuclear Magnetic Resonance). These methods have achieved successfully on the basic analysis of chains and layering structures of polymer nanocomposites. However, information on the molecular level cannot be provided by those approaches. MD (Molecular Dynamic) simulation method could be employed to develop further information on the molecular level about organoclays and interlayer structure polymer nanocomposites. In the research of ODTMA-MMT (Octadecyltrimethylammonium-Montmorillonite) organoclay simulation, we find that the strong layering behaviour of interlayer ODTMA molecules is present with the same minimum distance between nitrogen atoms and MMT surface in different T/O (Tetrahedral vs. Octahedral) ratio cases. Nitrogen atoms sit right above the corresponding hexagonal cavities, which is in agreement with the previous research. The interaction energy between surfactants and MMT clay will reach the lowest point when substitution ratio of tetrahedral and octahedral (T/O) is equal to 1:1. Moreover, MSD (Mean Square Displacement) and diffusion coefficient of different models under same CEC (Charge Exchange Capacity) condition are inverse ratio to the T/O proportion. In nylon6 polymer nanocomposites, sodium cations which exist originally in ensemble as charge balancer are absorbed much closer to MMT surface than the organic components in the nylon 6 ODTMA-MMT ensemble. Sodium atoms or nitrogen atoms in surfactants both have higher MSD and coefficients than those atoms in the organic-modified clays. In the exfoliated nylon 6 ODTMA-MMT nanocomposites, pair correlation has been analysed instead of density profile. Layering packing structure is also shown through this analysis, which is also consistent with previous work.