Molecular dynamics (MD) simulations have been used to investigate the interlayer structure of water saturated organoclays. The basal spacing values of cetyltrimethylammonium (CTMA) intercalated montmorillonite (CTMA-Mont) in dry and water saturated states were detected using XRD. Then the results were compared with simulation results of dry CTMA-Mont. The MD simulations show that the CTMA cations form layer structures on siloxane surface and aggregate in the interlayer space. Water molecules can access part of the siloxane surface and form H-bonds with surface oxygen atoms by donating one or two of the hydrogen atoms. Thus, the water molecules close to the surface have a preferred orientation with the dipole pointing towards the surface, while in the interlayer space, the water molecules aggregate to form large clusters. The H-bonds between surface oxygen and water molecules are shown to be slightly weaker than those between water molecules. Although water molecules within interlayer space can form strong H-bonds as in bulk water the number of H-bond for each water molecule is reduced. Our results indicate that MD simulations represent a useful tool for exploring the microstructure of water saturated organoclays.