Using scanning tunneling microscopy and density functional theory, we show that the molecular ordering and orientation of metal phthalocyanine molecules on the deactivated Si surface display a strong dependency on the central transition-metal ion, driven by the degree of orbital hybridization at the heterointerface via selective p-d orbital coupling. This Letter identifies a selective mechanism for modifying the molecule-substrate interaction which impacts the growth behavior of transition-metal-incorporated organic molecules on a technologically relevant substrate for silicon-based devices.