In this paper, we present molecular dynamics (MD) simulations of interfaces composed of self-assembled monolayers (SAMs) and solvents in order to investigate the heat transfer characteristics at the interface. Two typical normal alkylthiolate SAMs with different chain lengths, i.e., 1-propanethiol C(3)H(7)SH and 1-dodecanethiol (C(12)H(25)SH) chemically adsorbed on Au(111) substrate surfaces, were used, and toluene was adopted as the organic solvent. In addition to the SAM systems, an interface composed of the bare solid substrate and solvent (without SAMs) was analyzed for comparison. Nonequilibrium MD simulations, in which a temperature gradient perpendicular to the interface was imposed, were performed and the difference in thermal boundary resistance in the interface systems was discussed. We observed that the SAM interfaces have smaller thermal resistance when compared with that of the bare solid interface. In order to understand the mechanisms of the small resistance at the SAM-solvent interfaces, the vibrational character of molecules in each phase, which contacted each other at the interface was analyzed and a detailed adsorbed structure of solvent molecule in the interface region was extracted. As a result, a clear difference in these characters was found between the SAM interfaces and bare solid interface.