Molecular dynamics (MD) simulations are considered to be an effective way to analyze the thermal behavior of nanocomposites for various components. In this study, we investigate the thermal conductivities of PDMS chains as well as the GNPs/PDMS composites by non-equilibrium molecular dynamics (NEMD) simulations. Firstly, the thermal properties of PDMS chains are calculated by taking account of the effects of temperature, length and number of chains. Then, a series of GNPs/PDMS composite models which have various PDMS chains are parallel to the surface of GNPs are proposed, and their thermal conductivities are studied in terms of the numbers and position of the chains. The simulation results show that the thermal conductivity of the PDMS chains linearly increases with their lengths and numbers. However, the temperature has minimum influence on thermal conductivity. The proposed GNPs/PDMS composite model with aligned GNPs/PDMS, which could avoid disordered and phonon scattering at interfaces has a huge increase in thermal conductivity compared to the PDMS chains. A case study shows that the position of the PDMS chains has effect on the thermal conductivity of GNPs/PDMS composites, and the PDMS chains in one side of GNPs has higher thermal conductivity than the PDMS chains in two sides of GNPs.