Controlled bottom-up fabrication of molecular nanostructures through on-surface reactions of tailor-made precursors is of scientific and technological interest. Recently, on-surface polymerization reactions influenced by precursor self-assembly have been reported. Thus, a fundamental understanding of the reaction process is a prerequisite for controlled formation. Herein, we report on the influence of molecular self-assembly of dibrominated hexaphenylbenzene (Br2-HPB) on the on-surface polymerization reactions on a Au(111) substrate. By using low-temperature scanning tunnelling microscopy (STM), we find that the polymerization of Br2-HPB proceeds while maintaining the long-range ordered self-assembly, despite a decrease in HPB-HPB distance due to debromination and successive covalent bonding of Br2-HPB. From the STM investigations of the polymerization process, we conclude that the polymerization of Br2-HPB is accompanied by molecular rotations to maintain the periodic array of the self-assembled structure, contrary to the conventional understanding of the polymerization of the self-assembled precursor layer.