Thermal conductivity of polymer-based (nano)composites is typically limited by thermal resistances occurring at the interfaces between the polymer matrix and the conductive particles as well as between particles themselves. In this work, the adoption of molecular junctions between thermally conductive graphene foils is addressed, aiming at the reduction of the thermal boundary resistance and eventually lead to an efficient percolation network within the polymer nanocomposite. This system was computationally investigated at the atomistic scale, using classical Molecular Dynamics, applied the first time to the investigation of heat transfer trough molecular junctions within a realistic environment for a polymer nanocomposite. A series of Molecular Dynamics simulations were conducted to investigate the thermal transport efficiency of molecular junctions in polymer tight contact, to quantify the contribution of molecular junctions when graphene and the molecular junctions are surrounded by polydimethylsiloxane (PDMS) molecules. A strong dependence of the thermal conductance was found in PDMS/graphene model, with best performances obtained with short and conformationally rigid molecular junctions. Furthermore, the adoption of the molecular linkers was found to contribute additionally to the thermal transport provided by the surrounding polymer matrix, demonstrating the possibility of exploiting molecular junctions in composite materials.