In this study, the effects of a backbone chemical structure on the characteristics of supramolecular polymers based on 2-ureido-4[1H]-pyrimidinone (UPy) moiety with quadruple hydrogen bonding were investigated. The supramolecular polymers were easily synthesized via a UPy moiety functionalized oligomer with a molar mass of approximately 3,000 g/mol. The oligomers selected to form the supramolecular polymers included polytetramethylene glycol (PTMG), polycaprolactone diol (PCL), and polycarbonate diol (PC). The characteristics of the UPy moiety functionalized oligomer are highly dependent on the mobility of the backbone and the existence of the UPy cluster, which is formed by stacking between adjacent UPy dimers. The PC-based supramolecular polymers yielded higher UPy stacked crystals (induced by the UPy cluster) than the PTMG and PCL-based supramolecular polymers.