We measure the room temperature thermal conductance of interfaces between an archetypal organic semiconductor copper phthalocyanine (CuPc) and several metals (aluminum, gold, magnesium, and silver) using the 3-omega method. The measured thermal boundary conductance (TBC) scales with bonding strength at the CuPc-metal interface, a correlation that is supported by molecular dynamics (MD) simulation, allowing the extrapolation of the effective interface Young's modulus. The trend in modeled interface modulus is in agreement with that deduced from adhesion tests, e. g., approximately 2 GPa for CuPc-gold and CuPc-silver interfaces, comparable to the van der Waals interaction strength of the materials. Using MD simulations in which the effects on thermal transport can be studied as a function of interfacial bond strength only, we isolate the relative contribution of acoustic mismatch and interface bond strength to TBC. Furthermore, measurements and modeling of organic/organic (e. g., CuPc/C-60) interfaces reveal that the TBC of this system is not as sensitive to bonding strength as the CuPc/metal system, due to a larger overlap in the phonon density of states in the low frequency regime, despite the weak bonding between organic layers. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4759286]