Successful thermal management in nanostructured devices relies on control of interfacial thermal transport. Recent measurements have revealed poor thermal transport across interfaces between two dissimilar materials, e.g. organic semiconductors and metals. In such systems, the interfacial thermal conductance, G b , is dominated by the strength of interfacial bonding, but existing analytical models still fail to accurately predict G b , especially for organic-metal interfaces.Growing interest in this research area calls for comprehensive understandings of interfacial thermal transport across hybrid material interfaces. Here we demonstrate that spatial nonuniformity has to be assessed in the calculation of G b for interfaces with partial coverage or incommensurate growth that is characteristic of these interfaces. The interface between copper phthalocyanine (CuPc) and F.C.C metals (Ag, Al, Au) exhibits a six-fold difference between the metal's (~ 4 Å) and organic molecule's (~ 25 Å) lattice constant. Molecular dynamics simulations reveal the spatial variation of G b , and a model is developed that considers the spatial variations in phonon transmission, successfully predicting G b for many organic-metal interfaces.