The source regions of the Yangtze and Yellow Rivers on the Tibetan Plateau provide vital water resources for downstream ecosystems and populations, yet their runoff responses to climate warming remain insufficiently understood. Based on daily runoff data from six hydrological stations in the Yellow and the Yangtze River basins during 1980–2023, this study investigates the evolution and relatively stronger statistical climatic association of runoff in the source regions of the Yangtze and Yellow Rivers. The results indicate that annual runoff exhibited an overall increasing trend, primarily driven by a significant increase in non-flood-season runoff, while flood-season runoff increased insignificantly; Low runoff indices increased significantly at most stations, reflecting enhanced low-flow conditions and increased dry-season water availability, whereas high runoff indices showed no significant trends; wavelet analysis identified dominant periodicities of approximately 13.5 and 4.8 years. Furthermore, it indicates that precipitation remains the relatively stronger partial statistical climatic association for flood-season runoff throughout the study period, with its statistical association continuously strengthening. However, under climate warming, the influence of temperature on runoff is also gradually intensifying. The preceding cold season has exhibited an increased statistical contribution of temperatures, although concurrent warm-season precipitation maintains a stable statistical contribution. These findings carry significant implications for sustainable water resource management and climate adaptation in the Asian Water Tower, underscoring the necessity to incorporate changing climatic associations into long-term hydrological planning to safeguard downstream water security and ecosystem services.