One-dimensional nanoparticles (1D NPs), such as single-wall carbon nanotubes (SWNTs) and metallic, semiconducting, and magnetic nanorods, have received great attention due to their unique anisotropic physical properties, which provide a wide range of potential applications such as optical and electronic devices, sensing and imaging, energy storage, and drug delivery. For practical realization of 1D NPs for a variety of potential applications, it is essential to fabricate a well-defined symmetric, directional, hierarchical structure using molecular self-assembly. Studies on the fabrication of hierarchical structures of 1D NPs have been successfully done by using various self-assembling method including solvent evaporation, electrostatic attraction, and DNA programming. However, 1D NP binary superlattice, which is expected to show emerging properties through collective interaction between different NPs, has not been reported so far. In this paper, first, a binary superlattice of 1D NPs has been developed for the first time using a hydrophillically functionalized SWNTs and a pre-foremd hexagonal phase of cylindrical micelles. The combination of small angle neutron and x-ray scattering measurements shows that a $AB_2$ type binary superlattice, in which the hexagonal structure of functionalized SWNTs are embedded in honeycomb lattice of cylindrical micelles, are formed. The $AB_2$ type binary superlattice of 1D NPs can be highly aligned into one direction under an oscillatory shear field. Theoretical calculation based on the cell theory shows that the $AB_2$ and $AB_3$ type binary superlattices can be formed to maximize the free volume entropy for both 1D NPs of two different diameters depending on the diameter and mixing ratios. Second, the self-assembly phenomenon of binary mixtures of cylindrical colloids with different diameters under the depletion attraction has been investigated. By varying on the diameter ratio, mixing ratio, and repulsive or attractive force between the different cylindrical colloids, it is proved that the weak attraction is necessary to form the hierarchical structure in addition to the diameter and mixing ratios. Third, based on the understanding of the interactions between different 1D NPs obtained above studies, a facile method to fabricate two-dimensional hexagonal monolayer superlattices of gold nanorods (GNRs) individually embedded in silica matrix on substrate has been developed. In this method, the cetyltrimethylammonium bromide (CTAB) bilayer-coated GNRs are self-assembled into a hexagonally packed monolayer superlattice on substrate by slow evaporation in the presence of silica precursors in the solution at a highly acidic condition. The GNR superlattices fabricated by this method show an excellent structural stability at high temperature as high as $500^\circ C $ and in solvents of a wide range of polarities including water, ethanol, toluene and cyclohexane. The structural stability makes the GNR superlattices highly reusable SERS active substrates for sensitive molecular detection, well-maintaining the SERS intensity over 10 cycles. The understanding of interparticle interactions between different 1D NPs and self-assembly of GNRs obtained in these studies may provide a new route to fabricate the binary superlattice of GNRs, which is highly stable, and thus, can be applied in various application fields.