Understandings heat transfer across a solid/liquid interface is crucial for establishing novel thermal control pathways in a range of energy applications. One of the major problems raised in this context is the impact of the three-phase contact line between solid, liquid, and gas on heat flux perturbations at the nanoscale. The focus of this research is the thermal transport via nanosized meniscus restricted between two solid walls. The molecular dynamics approach was used to consider different wetting states of the meniscus by varying the interaction potential between atoms of the substrate and the liquid. The influence of the meniscus size on the energy exchange between two solid walls was also studied. It was discovered that possessing a three-phase contact line reduces the interfacial boundary resistance between solid and liquid. Furthermore, the finite element method was employed to connect atomistic simulations with continuum mechanics. We show that the wetting angle and interfacial boundary resistance are essential important parameters for multiscale analysis of thermal engineering issues with precise microscale parametrization.