Supramolecular elastomers based on quaternary hydrogen bonding of ureido-pyrimidinone (UPy) groups own special properties such as reversibility, self-healing, and good processability, which can be used in many special fields. In this paper, a novel type of linear polyisoprene supramolecular elastomer (LPSE) was prepared via anionic polymerization by deliberately introducing hydroxyl, isocyanate, and UPy groups into the ends. The formation of supramolecular structure showed significant effects on the microphase structures of LPSE, which was characterized by Fourier-transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), hydrogen nuclear magnetic resonance (1H-NMR), and dynamic mechanical analysis (DMA). Results showed that the introduction of UPy groups played a certain role in the improvement of the thermal stability, toughness, and tensile strength of the elastomer. Moreover, from self-healing tests, the hydrogen bonds of UPy showed dynamic characteristics which were different from covalent sacrificial bonds and exhibited the reassociation phenomenon. This study can not only extend our understanding of the toughening effect of strong hydrogen bonds, but also help us to rationally design new and tough elastomers.