Vegetation phenology is a biological factor that directly or indirectly affects the dynamic equilibrium between water and carbon fluxes in ecosystems. Quantitative evaluations of the regulatory mechanisms of vegetation phenology on water–carbon coupling are of great significance for carbon neutrality and sustainable development. In this study, the interannual variation and partial correlation between vegetation phenology (the start of growing season (SOS), the end of growing season (EOS), and the length of growing season (LOS)) and ET (evapotranspiration), GPP (gross primary productivity), WUE (water use efficiency; water–carbon coupling index) in the Huang-Huai-Hai and Yangtze River Basins in China from 2001 to 2019 were systematically quantified. The response patterns of spring (autumn) and growing season WUE to SOS, EOS, and LOS, as well as the interpretation rate of interannual changes, were evaluated. Further analysis was conducted on the differences in vegetation phenology in response to WUE across different river basins. The results showed that during the vegetation growth season, ET and GPP were greatly influenced by phenology. Due to the different increases in ET and GPP caused by extending LOS, WUE showed differences in different basins. For example, an extended LOS in the Huang-Huai-Hai basins reduced WUE, while in the Yangtze River Basin, it increased WUE. After extending the growing season for 1 day, ET and GPP increased by 3.01–4.79 mm and 4.22–6.07 gC/m2, respectively, while WUE decreased by 0.002–0.008 gC/kgH2O. Further analysis of WUE response patterns indicates that compared to ET, early SOS (longer LOS) in the Yellow River and Hai River basins led to a greater increase in vegetation GPP, therefore weakening WUE. This suggests that phenological changes may increase ineffective water use in arid, semi-arid, and semi-humid areas and may further exacerbate drought. For the humid areas dominated by the Yangtze River Basin, changes in phenology improved local water use efficiency.