The thermal boundary conductance between water and self-assembled monolayer was studied using nonequilibrium molecular dynamics simulations. Different thermal transport behaviors were observed for hydrophobic and hydrophilic self-assembled monolayers. In the temperature range between 280 and 340 K, the thermal boundary conductance was found to depend on the temperature for hydrophobic self-assembled monolayers. On the contrary, the difference in thermal boundary conductance at different temperatures was slight for hydrophilic self-assembled monolayers. The correlations in velocity and density between terminal atoms of self-assembled monolayer and water molecules within the interface region were analyzed to understand the mechanism of thermal transport across the interface. The vibrational density of states calculation indicated that the temperature dependence does not originate from the overlap of phonon spectrum. The analysis of radial density distribution revealed that the temperature dependence is mainly attributed to the number of water molecules surrounding the terminal atoms of self-assembled monolayers.