In this study, we investigated the thermoelectric properties of molecular junctions, created by trapping naphthacene (C18H12) and rubrene (C42H28) molecules between two graphene electrodes. It is found that the charge transport of naphthacene-based and rubrene-based graphene junctions is not sensitive to the introduction of edge side branches or the increase in molecular length and still maintains resonance transport at the Fermi level. Notably, the presence of pendant branches on the molecular trunk in rubrene-based graphene junctions leads to a suppression of phonon transport, attributed to multiple scattering at the branch attachment points or Fano resonance scattering. The phonon thermal conductance of the rubrene junctions can be reduced by nearly half compared to that of naphthalene junctions. Furthermore, the room-temperature figure of merit (ZT) is significantly enhanced from 0.2 to 1.1 upon constructing weak coupling junctions, representing an almost tenfold increase over covalent junctions. These findings mean that it is highly desirable to find a mechanism that can suppress the phonon thermal conductance of self-assembled molecular films, while preserving their power factor at optimal levels to obtain high-efficiency thermoelectric performance.