Two-dimensional (2D) nanomaterials have attracted intensive interest in the past decades owing to their superior properties and prospective applications in nanodevices. Recently, there is an increasing demand for understanding the thermal properties of these nanomaterials. This demand is driven by the fact that thermal dissipation at the nanoscale has become a crucial issue because of the ever continuing miniaturization of nanodevices. In addition, thermal transport in nanomaterials has revealed many unique phenomena, of which the understanding would lead to novel nanotechnologies in thermal management. Most of these unique phenomena are related to an important characteristic of nanomaterial: their properties highly depend on their atomic structures which are often inevitably altered by chemical functionalization, strain and presence of structural interruptions induced during fabrication or application. Hence, this PhD study has been devoted to studying the thermal properties of 2D nanomaterials and understanding the structural alteration effects through the method of non-equilibrium molecular dynamics simulation. Three representative types of such 2D nanomaterials, namely, graphene (GE), silicene (SE) and MoS 2 have been investigated. As one of the important chemical functionalization methods, hydrogenation has been widely used to tune the properties of nanomaterials and obtain their derivative counterparts. The simulation results have revealed that the thermal conductivity of hydrogenated GE is much lower than that of pristine GE and highly depends on both the hydrogen coverage and hydrogenation pattern. The two distinct mechanisms of phononinterface and phonon-phonon scatterings were identified to be responsible for the low