Structural ordering is widely present in molecules and materials. However, the organization of molecules on the curved surface of nanoparticles is still the least understood owing to the major limitations of the current surface characterization tools. By the merits of x-ray crystallography, we reveal the structural ordering at all scales in a super robust 133–gold atom nanoparticle protected by 52 thiolate ligands, which is manifested in self-assembled hierarchical patterns starting from the metal core to the interfacial –S–Au–S– ladder-like helical “stripes” and further to the “swirls” of carbon tails. These complex surface patterns have not been observed in the smaller nanoparticles. We further demonstrate that the Au133(SR)52 nanoparticle exhibits nonmetallic features in optical and electron dynamics measurements. Our work uncovers the elegant self-organization strategies in assembling a highly robust nanoparticle and provides a conceptual advance in scientific understanding of pattern structures.