Surface-modified gold nanorods (Au NRs) with 1,2-dipalmitoyl- sn-glycero-3-phosphothioethanol (DPPTE) were synthesized, and their self-assembled structures on a silicon substrate were observed using a scanning electron microscope (SEM). The Au NR-DPPTE complex formed characteristic one- and two-dimensional self-assemblies induced by intermolecular interactions of surface-anchored lipids via simple drying process. The interparticle distance between neighboring NRs was uniform at around 5.0 nm, which was consistent with the thickness of the lipid bilayer. Furthermore, we observed the anisotropic configurations of the NR complex, preferentially oriented in a lateral or perpendicular fashion, in a two-dimensional assembled structure dependent on the interfacial hydrophilicity or hydrophobicity of the silicon surface.