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The purpose of this study is to address the problem of reconstructing damaged styrene–butadiene–styrene (SBS) molecular structures in order to facilitate the effective recycling of aged SBS-modified asphalt (SBSMA). Traditional experimental methods face challenges when attempting to investigate the reconstruction process and reaction mechanism of aged SBS molecules. To explore the reaction mechanism of aged SBSMA with active rejuvenators and to promote the recycling of aged SBSMA, this study employs molecular dynamics and quantum chemistry to investigate the reconstruction process of the damaged SBS molecular structure using two reactive compounds, namely, methylene diphenyl diisocyanate (MDI) and toluene diisocyanate (TDI), from a molecular perspective. The results showed that the carbon–carbon double bonds in the SBS molecules are susceptible to oxidation, leading to the formation of hydroxyl and carboxyl groups. The reaction between the hydroxyl groups in aged SBS and TDI can spontaneously proceed, while the reaction between the carboxyl groups and MDI can also spontaneously proceed. When the proportion of hydroxyl groups in aged SBS molecules is higher, TDI can be the preferred choice for reconstructing aged SBS molecules. Conversely, when the aged SBS molecules contain more carboxyl groups, MDI can be selected as the better reactive compound. By reconnecting the aged SBS molecules, the need for new SBSMA can be reduced, leading to lower demand for original resources, extended material service life, reduced waste generation, and effective resource recycling. This study provides a new method to explore the problem of SBS molecular structure damage reconstruction and offers a possible mechanism explanation of reaction between aged SBS molecules and reactive compounds. These findings are expected to promote the sustainable development and environmental applications of SBSMA. [ABSTRACT FROM AUTHOR]