Manipulating and controlling heat flow across the interface between two materials is a significant issue for modern devices and materials where the small length scales result in a high density of interfaces that dominate the effective thermal conductivity (k). To control nanoscale heat transport between dissimilar materials, a deeper understanding of how the underlying chemistry and interfacial structure manipulates the thermal boundary conductance (TBC) of the interface is required. While many experimental techniques have been described for studying thermal transport in thin films, and specifically polymer nanocomposites, there is a lack of experimental investigations that can directly link the interfacial bonding to the resulting TBC between amorphous materials. The dearth of experimental data is caused by poor TBC measurement sensitivity in the case of the single interface in a substrate-supported polymer thin film structure due to the low polymer intrinsic thermal conductivity and due to the complexity of the analysis in the case of particle-polymer nanocomposites with high interfacial density. Separately, particle-based nanocomposites tend to have an unstable structure as the relative strength of particle-particle and particle-polymer interactions determines the dispersion of particles throughout the nanocomposite. As a result, changes in the TBC of the particle-polymer interfaces in the nanocomposite becomes highly convoluted with changes to the particle dispersion and particle-particle contact. In this study, we show that the thermal conductivity of a polymer-glass nanocomposite with polymer molecules under nanometer scale confinement in an organosilicate matrix can be characterized using time-domain thermoreflectance spectroscopy. The thermal conductivity characterization is made possible by the ultra-high internal interfacial density and can be further quantitatively linked to the nature of the organosilicate matrix surface chemistry. The TBC at the polymer-organosilicate interface is extracted by comparing the measured thermal conductivity with effective medium and numerical model calculations. Fourier transform infra-red spectroscopy and X-ray photoelectron spectroscopy (XPS) were used to characterize the hydrogen bonding between the polymer molecules and organosilicate matrix. Thin-film fracture measurements were used to quantify the molecular polymer bridging contribution to the cohesive fracture resistance and its dependance on interfacial bonding. This new experimental metrology provides a direct experimental link between thermal and mechanical properties and the nature of interfacial bonding between polymer molecules and surfaces.