Nanomaterials have been actively employed in various applications for energy and sustainability, such as biosensing, gas sensing, solar thermal energy conversion, passive radiative cooling, etc. Understanding thermal transports inside such nanomaterials is crucial for optimizing their performance for different applications. In order to probe the thermal transport inside nanomaterials or nanostructures, tip-based nanoscale thermometry has often been employed. It has been well known that phonon transport in nanometer scale is fundamentally different from that occurred in macroscale. Therefore, Fourier's law that relies on the diffusion approximation is not ideally suitable for describing the phonon transport occurred in nanostructures and/or through nanoscale contact. In the present study, the gray Boltzmann transport equation (BTE) is numerically solved using finite volume method. Based on the gray BTE, phonon transport through the constriction formed by a probe itself as well as the nanoscale contact between the probe tip and the specimen is investigated. The interaction of a probe and a specimen (i.e., treated as a substrate) is explored qualitatively by analyzing the temperature variation in the tip-substrate configuration. Besides, each contribution of a probe tip, tip-substrate interface, and a substrate to the thermal resistance are analyzed for wide ranges of the constriction ratio of the probe.