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 Au92(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 × 2) symmetry. The Au-S binding mode and translational symmetry in the kernel and on the surface of the Au92 nanocrystal can be generalized infinitely to construct the bulk two-dimensional SAMs and various tetragonal nanocrystals.