Multifunctional nanocomposite materials have been used extensively in aerospace, mechanical, civil engineering industries, and other engineering applications. This is mainly due to the enhanced mechanical characteristics such as high strength-to-weight ratio and the unique thermal and physiochemical properties of these nanostructures. It has been reported that there are significant improvements in the thermal conductivity of composite structures with the addition of low volume fractions of graphene. To understand and develop efficient composite systems with desired thermal characteristics, it is necessary to develop accurate thermal transport models of these advanced composite systems. In this chapter, the authors discuss some of the recent developments in multiscale modeling of the thermal and mechanical properties of advanced nanocomposite systems. To enhance the theoretical model development discussed in this chapter, the authors have also included some relevant works from the literature.