In this paper, we perform molecular dynamics simulations of self-assembled monolayer (SAM) and solvent interfaces in order to elucidate the microscopic mechanisms of interfacial heat transfer at the SAM interfaces. Archetypal SAM systems, i.e., n-alkanethiol chemically adsorbed on Au (111), and toluene solvent are employed in our simulations. By using nonequilibrium molecular dynamics technique, a temperature gradient is imposed perpendicular to the interface, and interfacial heat transfer characteristics are analyzed. In addition to the SAM systems, a bare solid substrate and solvent system is examined to compare thermal boundary resistances at the SAM-modified interface and non-modified one. As a result, we find a significant decrease of the thermal boundary resistance at the SAM-toluene interface as compared to that of the bare Au interface. In order to explain this effect, we focus on the adsorption structure of toluene in the vicinity of the interface.