Three kinds of pi-conjugated perylenetetracarboxylic diimide (PTCDI)-based organic functional derivatives, i.e., N,N'-di(2-ethylhexyl)-3,4,9,10-perylene diimide (molecule 1), N,N'-di(2-ethylhexyl)-1,7-dithi en-2-yl-3,4,9,10-perylene diimide (molecule 2), N,N'-di(2-ethylhexyl)-1,7-di(2-bromothien-5-yl)-pery lene-3,4,9,10-perylene diimide (molecule 3), have been prepared and investigated by using a scanning tunneling microscopy under ambient conditions. All of them can form long-ranged ordered self assembled monolayer (SAM) with two different phase structures on highly oriented pyrolitic graphite (HOPG) surface. Coexistence of the two phases in the formed SAMs depends strongly on cooperation of various interactions including the molecule-substrate and molecule-molecule. Orientation of the molecular perylene cores primarily governs the molecular orientation in the SAMs by 7t-ic interaction of the molecule-substrate through uttermost matching the graphite surface lattice. At the same time, the branched alkyl-chain substituents at N-sites can adjust intermolecular distances through conformation change while cyclic It-conjugated substituents at bay-positions lead to molecular rotation movement on HOPG, driven by the decreased molecule-substrate interaction caused by distortion of the perylene cores and the intermolecular interaction among the adjacent bay-substituents with rotation conformation change. In addition, the lateral forces from rotation conformation change of the bay-position substituents can also be strong enough to keep the orientation of the perylene cores unchanged. DFT calculation results further reveal the formation mechanisms for the three molecular self-assembly systems. These findings distinctly show that the SAM structures based on the 7t-conjugated PTCDI-based organic functional derivative molecules can be precisely modulated through introducing suitable substituents at both N- and bay-positions on the PTCDI core. (C) 2017 Elsevier Inc. All rights reserved.