Self-assembled monolayers (SAMs) of large pi-conjugated aromatic thiols, 1-mercaptopyrene (MP), 6-mercaptobenzo[a]pyrene (MBP), and 1-(11-mercaptoundecyl)pyrene (MUP), prepared on Au(111) substrate at different temperatures were investigated by scanning tunneling microscopy. At room temperature, only MP and MBP molecules formed well-ordered SAMs with [Formula: see text] and ([Formula: see text]) Rect symmetry, respectively. In contrast, MUP molecules were adsorbed randomly on the surface. At elevated temperatures, all three molecules produce well-ordered SAMs. At 343 K, the structure of MBP remains unchanged, while MP and MUP molecules undergo thermally induced rearrangement to form a ([Formula: see text]) Rect symmetry due to improved ordering and denser packing. The results from the systematic study of controlled self-assembly of a series of pyrene-based thiols provide insights on the molecular structure-dependent and temperature-dependent organization of large pi-conjugated aromatic thiols to obtain ordered SAMs.