In the present study, we investigate single mode phonon scattering from a junction structure that is consisted of a (6,6) single walled carbon nanotube (SWCNT) and graphene under mechanical deformation using phonon wavepacket analysis. Longitudinal acoustic phonon mode is selected since it is the most important thermal energy carrier in carbon-based nanomaterials. The results show a large phonon scattering from the junction at all frequencies (0.5 ∼ 8 THz) and a significant amount of phonon energy (nearly 40%) is absorbed by the graphene floor between the SWCNT-graphene junctions. It is interesting to note that the phonon energy is better absorbed by the SWCNT-graphene junction while the amount of energy reflection is decreased when the structure is mechanically deformed. Additionally, the amount of energy reflection is higher at lower frequencies when the structure is mechanically deformed while the energy transmission becomes slightly higher at higher frequencies when the structure is deformed. Since high frequency phonons are populated more at high temperatures, it is expected that thermal transport through a deformed SWCNT-graphene junction becomes more efficient at high temperatures when compared to an undeformed SWCNT-graphene junction structure. However, thermal transport through a deformed junction is expected to be less efficient at low temperatures when compared to an undeformed junction structure since most of the phonons populated at low temperatures possess low frequencies (or long wavelengths). Group velocity is closely related to the energy absorption in the graphene floor between two SWCNT-graphene junctions; higher group velocity generally facilitates a better absorption by the graphene floor. The results obtained in the present research study will accelerate the development of futuristic electronics by providing a tool for synthesizing novel carbon nanostructures that ensure efficient thermal performance under mechanical deformation.