This study examined the interfacial heat condition between a poly(ethylene glycol) (PEG) self-assembled monolayer (SAM) and water using molecular dynamics simulation. It was found that the PEG SAM has higher thermal boundary conductance (TBC) than the traditionally used alkane-based SAM. The TBC conditionally varied with the length of the PEG molecules, where interfacial thermal resistance was a key factor. Our results reveal that the TBC of the PEG SAM/water interface is greatly influenced by its structural properties rather than the matching of vibrational properties between the SAM terminal and water. The structural analysis shows that the water structure around the terminal oxygen atom of the SAM plays a vital role in controlling the TBC. In this study, the concept of free volume has also been exploited, and the result suggests that the reduction of the free volume fraction accommodates a higher TBC. The model was precisely validated against experimental data by calculating the tilt angle and dihedral angle of the PEG SAM, the persistence length of the PEG chain in the water medium, and the sulfur position of the PEG SAM headgroup on the gold surface using quantitative scanning transmission electron microscopy image simulation.