The ability to precisely control the self-assembly of colloidal nanoparticles into desired and tunable superstructures holds immense potential, but achieving this remains a challenge due to intricate interplay of various controlling factors that govern this process at the nanoscale. Here, we demonstrate the controlled fabrication of co-existing smectic and triangular crystalline phases of gold nanorods, separated by domain boundary, by fine tuning the interparticle and particle–substrate interaction. The interaction forces between nanorods is tailored via the addition of surfactant, cetyltrimethylammonium bromide (CTAB), which in turn affects the particle–substrate attraction through screened electrostatic potential due to surfactant adsorption on the substrate. The emergence of the resulting phases is discussed via simulation of a coarse-grained model which considers the nanorod superlattices as nematic liquid crystals. It accounts for the interplay of repulsive, attractive forces, and particle–substrate interactions. The co-existing superlattice structures are obtained at low particle concentration over a large length scale, paving the way for various potential applications that specifically require both smectic and vertical rods on the same substrate.