In this article, we report the self-assembly process, structural features, thermal and hydration properties of the gold fullerene nanocomposite at room temperature by applying molecular dynamics simulation technique. The gold-fullerene systems constituting alkanethiol capped gold nanoparticle and pristinefullerene in explicit water have been simulated to gain insights on the influence of the terminal methyl (hydrophobic) and hydroxy (hydrophilic) groups on their structure and properties. The physisorption of the fullerene molecule into the thiol layer of the gold nanoparticle has been demonstrated and elucidated. Thechemical functionality of the terminal groups was found to affect the structure, specific heat capacity and the wetting behavior of the gold-fullerene nanocomposite. The findings from this computational study may aidthe understanding and development of novel gold-fullerene nanostructures for modulating their structural, thermal and hydration properties through the modification of their surface functional groups