Molecular junctions are promising candidates for thermoelectric devices due to the potential to tune the electronic and thermal transport properties. However, a high figure of merit is hard to achieve, without reducing the phononic contribution to thermal conductance. Here, we propose a strategy to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded π-stacked systems. Using first-principles calculations, we find that the thermal conductance of π-stacked systems can be reduced by about 95%, compared with that of a covalently bonded molecular junction. Phonon transmission of π-stacked systems is largely attenuated in the whole frequency range, and the remaining transmission occurs mainly below 5 THz, where out-of-plane channels dominate. The figure of merit (ZT) of the π-stacked molecular junction is dramatically enhanced because of the very low phononic thermal conductance, leaving room for further optimization of the electronic properties. (Figure Presented).