Under the ongoing trend of climate warming and increasing humidity on the Qinghai–Tibet Plateau, the Three River Source Region (TRSR) has shown strong sensitivity to global climate change. Its vegetation change is particularly worthy of attention and research. The Normalized Difference Vegetation Index (NDVI) is a key indicator for assessing the growth status of vegetation. However, the insufficiency of existing NDVI datasets in terms of spatiotemporal continuity has limited the accuracy of long-term vegetation change studies. This study proposed a machine learning-based downscaling framework that integrates the Moderate-resolution Imaging Spectroradiometer (MODIS) NDVI and the Global Inventory Monitoring and Modeling System (GIMMS) NDVI data to reconstruct a long-term, high-resolution NDVI dataset. Unlike conventional statistical fusion approaches, the proposed framework employs machine learning-based nonlinear relationships to generate long-term, high-resolution NDVI data. Three machine learning algorithms—Random Forest (RF), LightGBM, and CatBoost—were evaluated. Their performance was validated using the MODIS NDVI as reference, with the coefficient of determination (R²), root mean square error (RMSE), mean absolute error (MAE), and Pearson’s correlation coefficient (R) as evaluation metrics. Based on model comparison, the CatBoost model was identified as the optimal algorithm for spatiotemporal data fusion (R² = 0.9014, RMSE = 0.0674, MAE = 0.0445), significantly outperforming RF and LightGBM models and demonstrating stronger capability for NDVI spatiotemporal reconstruction. Using this model, a long-term, 1 km monthly GIMMS-MODIS NDVI dataset from 1982 to 2014 was successfully reconstructed. On the basis of this dataset, the spatiotemporal variation characteristics of vegetation in the TRSR from 1982 to 2014 were systematically analyzed. The research results show that: (1) The constructed long-series high-resolution NDVI dataset has a high consistency with MODIS NDVI data; (2) From 1982 to 2014, the NDVI in the TRSR showed an increasing trend, with an average growth rate of 0.0020/10a (p < 0.05). NDVI showed obvious spatial heterogeneity, characterized by a decreasing gradient from southeast to northwest. (3) The Yellow River source exhibited the most evident vegetation recovery, the Yangtze River Source area showed a moderate improvement, whereas the Lancang River Source area displayed little noticeable change. (4) Broad-leaved forests experienced the most significant growth, while cultivated vegetation displayed a marked tendency toward degradation. This study provides both a high-accuracy long-term NDVI product for the TRSR and a methodological foundation for advancing vegetation dynamics research in other high-altitude regions.