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This article explores the transverse thermal conductance between two parallelbonded as well as nonbondedcarbon nanotubes, embedded in an epoxy matrix using nonequilibrium molecular dynamics simulations. Here, we study the effect of different organic linkersconnecting the two nanotubeson the thermal interface conductance and compare these results with those of nonbonded nanotubes. Our results suggest that incorporation of linker molecules significantly modifies overall interface conductance between nanotubes. Specifically, we find that the conductance increases with the number of linking functionality but shows an opposite trend with respect to the linker’s length, that is, the longer the linker is, the lower the conductance. We attribute this behavior to weakening of van der Waals interactions between carbon nanotubes in the case of longer linkers as well as possible scattering of thermal vibrations …