Two-dimensional or three-dimensional highly ordered arrays of anisotropic nanoparticles provide attracting properties that are highly desired by the industry. Traditional assembly methods such as evaporation usually produces the nanostructure arrays only up to the millimeter scale with poor control of nanoparticle orientation, making them hardly applicable for industrial needs. Here, we report a facile method to assemble centimeter-scale gold nanorod (Au NR) arrays with highly controlled nanoparticle orientation and high reproducibility. We selectively functionalized the transverse or longitudinal facets of Au NRs with polyethylene glycol (PEG) molecules and utilized the interfacial polymeric affinity between the PEG domains on Au NRs and the PEGylated substrate to achieve the anisotropic self-assembly. The side-PEGylated Au NRs formed closely packed horizontal arrays, whereas the end-PEGylated Au NRs formed vertically standing arrays on the substrate, respectively. The obtained Au NR arrays with different orientations showed anisotropic surface-enhanced Raman scattering (SERS) performance. We showed that the vertically ordered Au NR arrays exhibited 3 times higher SERS signals than the horizontally ordered arrays.