Quantifying the spatial and temporal dynamics of carbon stocks in terrestrial ecosystems and carbon fluxes between the terrestrial biosphere and the atmosphere is critical to our understanding of regional patterns of carbon storage and loss. Here we use the General Ensemble Biogeochemical Modeling System to simulate the terrestrial ecosystem carbon dynamics in the Jinsha watershed of China's upper Yangtze basin from 1975 to 2000, based on unique combinations of spatial and temporal dynamics of major driving forces, such as climate, soil properties, nitrogen deposition, and land use and land cover changes. Our analysis demonstrates that the Jinsha watershed ecosystems acted as a carbon sink during the period of 1975–2000, with an average rate of 0.36 Mg/ha/yr, primarily resulting from regional climate variation and local land use and land cover change. Vegetation biomass accumulation accounted for 90.6% of the sink, while soil organic carbon loss before 1992 led to lower net gain of carbon in the watershed, and after that soils became a small sink. Ecosystem carbon sinks/source pattern showed a high degree of spatial heterogeneity, Carbon sinks were associated with forest areas without disturbances, whereas carbon Sources were primarily caused by stand-replacing disturbances. This highlights the importance of land-use history in determining the regional carbon sinks/source pattern.