Self-assembled monolayers (SAMs) are attracting attention as systems capable of nanoscale thermal management of material surfaces and interfaces. However, comprehensive studies, both experimental and theoretical, to facilitate quantitative understanding of thermal transport through SAMs remain rare. Here we focus on water/SAM/Au interfaces and present experimental and computational results on the effects of the structural factors of SAM-forming molecules on the interfacial thermal resistance (ITR). To evaluate the intrinsic ITR, we adopted an approach using tripodal triptycenes with thiol groups, which allows construction of SAMs with similar coverage and orientation on Au substrates, regardless of the type of functional group. We also address the effect of the number of thiol groups anchored to the Au surface, which is related to the heat flow path. Based on the structural characteristics of SAMs fabricated with these newly synthesized triptycene derivatives, their ITR values were determined by time-domain thermoreflectance measurements. The results were interpreted by computational simulations using nonequilibrium and equilibrium molecular dynamics methods, to provide a deeper insight into the ITR. The ITR decreases when functional groups capable of strong interactions with water molecules, such as hydrogen bonding, are present on the outermost layer of the SAM surface, whereas the presence of long-chain functional groups, even if hydrophilic, may cause thermal resistance. Thus, approaches using tripodal molecular motifs, such as triptycene, which allow the dense integration of hydrophilic functionality on a solid surface without relying on long-chain functional groups, could provide a solution for designing SAMs with small ITR.