We have studied the self-assembly structure of meso-diphenyltetrathia [22]-annulene [2,1,2,1] (DPTTA) on highly oriented pyrolytic graphite (HOPG), Au(111), and single-layer graphene (SLG) modified Au(111) substrates. High resolution scanning tunneling microscopy (STM) reveals that DPTTA molecules pack into one dimensionally ordered row structure on graphene and HOPG surfaces, while assemble into two dimensional close-packed structure on Au(111) surface. We ascribe this difference to the effect of the substrate. The addition of C-60 molecules on these DPTTA modified substrates further reveals that the structural difference in DPTTA adlayer can affect its ability to form donor-acceptor (D-A) hierarchical structure with C-60 molecules. The results provide an example of substrate effect in self-assemblies of functional molecules, which is significant for the design of molecular based devices. (C) 2016 Elsevier B.V. All rights reserved.