Waterproofing systems frequently experience performance degradation during long-term service due to material aging and structural deformation, thereby necessitating localized repair interventions. The bonding interface between newly applied and existing membrane materials is a critical determinant of repair effectiveness. In this study, the aging-dependent repair performance of three representative waterproof membrane systems was systematically investigated using peel strength testing, low-temperature flexibility assessment, and interfacial morphology analysis under thermal–oxidative aging for 2, 5, 14, and 28 days. The results demonstrate that the homogeneous repair system based on ultra-thin reinforced self-adhesive polymer-modified bituminous membranes exhibits superior overall performance, maintaining the highest peel strength with only minor degradation even after 28 days of accelerated aging. In contrast, the polymeric butyl self-adhesive membrane subjected to homogeneous repair exhibited rapid adhesion degradation after 14 days, whereas the heterogeneous repair system showed improved stability during intermediate aging stages. Low-temperature flexibility testing further revealed that root-resistant bituminous membranes exhibited a slower aging rate, with a cracking temperature increase of 7 °C after 28 days, compared to a 10 °C increase observed for ultra-thin self-adhesive membranes. These quantitative findings provide clear guidance for the selection of appropriate repair membrane systems under varying aging conditions in waterproofing engineering, particularly for maintenance and rehabilitation applications.