[Objective] The upper reaches of the Yellow River straddle the Qinghai-Tibetan Plateau and the Loess Plateau, providing a good platform for studying the mechanism of carbon storage dynamics under ecological-geographical differentiation. [Methods] The study of carbon stock dynamics and its driving mechanism is of great significance for regional sustainable development and future management. Taking the Taohe River Basin on the Qinghai-Tibetan Plateau and the Zuli River Basin on the Loess Plateau as study areas, the study explored the direct and indirect effects of climate, vegetation and water-sand on net primary productivity (NPP), and used elasticity coefficients and density analyses to quantify the thresholds of the effects of different factors on NPP. [Results] The mean values of NPP in the Tao River and Zuli River basins were 276.47 gC/m2 and 136.86 gC/m2, respectively, with significant differences in spatial distribution. The NPP of the Tao River Basin was greatly influenced by the moisture parameter, followed by the normalized vegetation index (NDVI), and the temperature (T) and soil erosion (A) showed negative effects and were relatively small. The NPP of the Zuili River Basin was most influenced by the NDVI and water retention (WR), and the T and A had the same negative effects on the NPP, but with a larger absolute value than that of the Tao River Basin. Spatially, the strongest explanatory power for the NPP distribution was found after the interaction of T and NDVI in both watersheds. Threshold quantification results varied among methods, with the thresholds for the effects of T and A on NPP being reached earlier in the Tao River Basin, and the thresholds for the effects of P, NDVI, and WR on NPP being reached first in the Zuili River Basin. [Conclusion] The driving force and threshold differences of carbon storage dynamics under different ecological and geographical differentiation are significant. Before reaching the "sustainable" threshold, there is no need for excessive human intervention, mainly through climate monitoring; However, when reaching the "restrictive" threshold, more attention needs to be paid to the purposeful and rational allocation of water resources, control of soil erosion, and mitigation of river sediment transport.