Molecular self-assembly of organic molecules on two-dimensional atomic crystals involves molecule–molecule interactions, molecule–surface interactions, or their combination. Most previous studies are focused on self-assembled organic monolayers. Here, for the first time, we report oriented organic nanowires self-assembled on a graphene surface in the atmosphere. Oriented lauroyl peroxide nanowires were formed when cooling down the melting lauroyl peroxide layer on a graphene surface but were not formed on SiO2 and copper surfaces. Structural analysis and theoretical simulation revealed that the combination of strong molecule–molecule packing interactions, weak molecule–molecule linking interactions, and weak molecule–surface interactions contributed to the formation of nanowires, while the orientation of nanowires depended on the six-fold rotational symmetry of graphene and strong molecule–surface interactions.