The Three-River Headwaters (TRH), which is the source area of Yangtze River, Yellow River and Lancang River, is vulnerable and sensitive, and its alpine ecosystem is considered an important barrier for China’s ecological security. Understanding the impact of climate changes is essential for determining suitable measures for ecological environmental protection and restoration against the background of global climatic changes. However, different explanations of the interannual trends in complex alpine ecosystems have been proposed due to limited availability of reliable data and the uncertainty of the model itself. In this study, the remote sensing-process coupled model (GLOPEM-CEVSA) was used to estimate the net primary productivity (NPP) of vegetation in the TRH region from 2000 to 2012. The estimated NPP significantly and linearly correlated with the above-ground biomass sampled in the field (the multiple correlative coefficient R2 = 0.45, significant level P < 0.01) and showed better performance than the MODIS productivity product, i.e. MOD17A3, (R2 = 0.21). The climate of TRH became warmer and wetter during 1990-2012, and the years 2000 to 2012 were warmer and wetter than the years1990-2000. Responding to the warmer and wetter climate, the NPP had an increasing trend of 13.7 g m-2 (10 yr)-1 with a statistical confidence of 86% (P = 0.14). Among the three basins, the NPP of the Yellow River basin increased at the fastest rate of 17.44 g m-2 (10 yr)-1 (P = 0.158), followed by the Yangtze River basin, and the Lancang River, which was the slowest with a rate of 12.2 g m-2 (10 yr)-1 and a statistical confidence level of only 67%. A multivariate linear regression with temperature and precipitation as the independent variables and NPP as the dependent variable at the pixel level was used to analyze the impacts of climatic changes on the trend of NPP. Both temperature and precipitation can explain the interannual variability of 83% in grassland NPP in the whole region, and can explain high, medium and low coverage of 78%, 84% and 83%, respectively, for grassland in the whole region. The results indicate that climate changes play a dominant role in the interannual trend of vegetation productivity in the alpine ecosystems on Qinghai-Tibetan Plateau. This has important implications for the formulation of ecological protection and restoration policies for vulnerable ecosystems against the background of global climate changes.