We present an overview of an approach to the thermal modeling of the grapheme-based nanostructures, and its implementation in high performance computing (HPC) system. As example of graphene-based nanosystem, a single electron transistor (SET) is discussed and the governing equations related to its structure are presented. The proposed approach is based on solution of the many-body Schrödinger equation and on the computation of the thermal conductivity using an HPC environment because of a lot of computations required for an accurate thermal analysis of a SET.