Addressing the issue of poor pavement performance in reclaimed asphalt mixture caused by the deterioration of aged asphalt properties, this study explores the use of triethoxy silane to convert strong polar carbonyl and sulfoxide groups in aged asphalt into hydroxyl groups. Simultaneously, low polarity ester or ether are generated. Subsequently, the hydroxyl groups are esterified with the end group deactivator isocyanate to achieve end group deactivation. The chemical repair mechanism was explored through analyzing the microcosmic chemical structure and polarity changes of aged asphalt at each repair stage. By comparing the results to matrix asphalt, the chemical repair effects of hydrogenation reduction and end-group deactivation on aged asphalt were evaluated by the analysis and testing of dynamic viscosity and low temperature properties of aged asphalt before and after repair. The results show that the chemical structure of aged asphalt is changed by hydrogenation and passivation. The carbonyl and sulfoxide groups in aged asphalt are reduced to hydroxyl groups by triethoxylsilane, which are then esterified to ester by isocyanate. After hydrogenation and passivation, the polarity of aged asphalt significantly weakens, leading to a substantial reduction in intermolecular forces and viscosity. Consequently, the low temperature deformation capacity is significantly improved. Furthermore, a strong correlation between low-temperature properties and the functional group index of aged asphalt was observd.