The nanostructures of a series of conjugated oligo(p-phenylene-ethynylene)s (OPE) adsorbed on a surface were thoroughly studied using scanning tunneling microscopy (STM). These oligomers have different backbone lengths and side chains. As a result, various nanostructures displaying periodic linear patterns at a single molecule level were obtained. Based on careful measurements on the STM images in combination with density functional theory (DFT) calculations, it could be found that the vertical and parallel distances between neighboring oligomers were responsible for the specific arrangement of the backbone and side chains. The results showed that these molecular designs strongly affect their self-assembled structure, which is important to clarify the structure-property relationship in the nanoscience field.