Topographic factors are recognized as one of the key factors influencing vegetation distribution patterns, and studying the interactions between them can contribute to enhancing our understanding of future vegetation dynamics. We used the Moderate-resolution Imaging Spectroradiometer Normalized Differential Vegetation Index (MODIS NDVI) image dataset (2000-2019), combined with Digital Elevation Model (DEM), and vegetation type data for trend analysis, and explored NDVI variation and its relationship with topographic factors through an integrated geographically-weighted model in the Three Parallel Rivers Region (TPRR) of southeastern Tibetan plateau in the past 20 years. Our results indicated that there was no significant increase of NDVI in the entire basin between 2000-2019, except for the Lancang River basin. In the year 2004, abrupt changes in NDVI were observed across the whole basin and each sub-basin. During 2000-2019, the mean NDVI value of the whole basin increased initially and then decreased with the increasing elevation. However, it changed marginally with changes in slope and aspect. We observed a distinct spatial heterogeneity in vegetation patterns with elevation, with vegetation in the southern regions showing higher NDVI than the north as a whole. Most of the vegetation cover was concentrated in the slope range of 8~35°, with no significant difference in distribution except flat-land. Furthermore, from 2000 to 2019, the vegetation cover in the TPRR showed an improving trend with the changes of various topographic factors, with the largest improvement area (36.10%) in the slightly improved category. The improved region was mainly distributed in the source area of the Jinsha River basin and the southern part of the whole basin. Geographically weighted regression (GWR) analysis showed that elevation was negatively correlated with NDVI trends in most areas, especially in the middle reaches of Nujiang River basin and Jinsha River basin, where the influence of slope and aspect on NDVI change was considerably much smaller than elevation.