In the present study, we performed molecular dynamics (MD) simulations of the self-assembled monolayer (SAM) interface system in order to investigate heat transfer characteristics over the SAM/alkane solvent interface. 1- dodecanethiol (C12H25S-) SAM chemisorbed on a gold substrate contacting with n-dodecane (C12H26) solvent was examined to compare the microscopic heat transfer mechanisms inside both the SAM and solvent phases. The direct nonequilibrium MD (NEMD) simulation, in which a constant heat flux across the SAM interface was imposed, was performed. The heat flux through the system was decomposed into the microscopic "building blocks", i.e., the contribution of energy transfer associated with molecular motion and that of energy exchange by intermolecular (nonbonded) and intramolecular (covalent bond) interactions. Interestingly, inside the SAM layer, almost all of the energy is transferred by the intramolecular interaction along the alkyl chain. On the other hand, in the alkane liquid phase, the intramolecular and intermolecular interactions have comparable contributions to the total heat flux in spite of the same molecular structure and alkyl chain length as the SAM molecules. This difference in the heat transfer mechanism implies the relation between the ordering structure of alkyl chains and thermal conductivity in organic materials.