We performed molecular dynamics (MD) simulations of the interface which is comprised of self-assembled monolayer (SAM) and water solvent to investigate heat transfer characteristics. In particular, local thermal boundary conductance (TBC), which is an inverse of so-called Kapitza resistance, at the SAM–solvent interface was evaluated by using the nonequilibrium MD (NEMD) technique in which the one-dimensional thermal energy flux was imposed across the interface. By using two kinds of SAM terminal with hydrophobic and hydrophilic properties, the local TBCs of these interfaces with water solvent were evaluated, and the result showed a critical difference due to an affinity between SAM and solvent. In order to elucidate the molecular-scale mechanism that makes this difference, microscopic components contributing to thermal energy flux across the interface of hydrophilic SAM and water were evaluated in detail, i.e., the total thermal energy flux is decomposed into the heat transfer modes such as the contribution of molecular transport and that of energy exchange by molecular interactions. These heat transfer modes were also compared with those in the bulk water.