Unveiling the ligand binding mode on the crystalline surfaces is important for deciphering the long-standing structural enigma in self-assembled monolayers (SAMs). Here, the binding and patterning structures of thiolates (SR) on the Au(100) crystalline facet are revealed on the basis of the atomic structure of a highly regular, single crystalline Au-92(SR)(44) nanocrystal. The six exposed facets of this tetragonal nanocrystal give rise to six pieces of "nanoSAMs". We found that thiolates bind to the planar (100) facets of the nanocrystal via a simple bridge-like mode and are assembled into an overlayer with c(2 X 2) symmetry. The Au-S binding mode and translational symmetry in the kernel and on the surface of the Au-92 nanocrystal can be generalized infinitely to construct the bulk two-dimensional SAMs and various tetragonal nano crystals.