Land use and land cover change (LULCC), along with the conversion of natural ecosystem cover into farmland, poses significant ecological challenges for desert riparian ecosystems. The Tarim River Basin (TRB), home to the world’s largest and most densely distributed and well-preserved desert riparian ecosystem, remains exceptionally susceptible to climate change. However, our understanding of the role of climatic factors (mean annual temperature (MAT); mean temperature during the warmest month (MWMT); relative humidity in September, October, and November (RH_SON); and the annual heat–moisture index (AHM)) in driving pattern changes in these ecosystems remains limited. To address this gap, we employed a transfer matrix approach coupled with geographically weighted regression models to conduct an extensive analysis of LULCC trends and their driving factors within the TRB from 1990 to 2020. The 30-year dataset on LULCC provided invaluable insights, revealing that the proliferation of farmland and shrubberies has precipitated the decline of arbor forests and grassland expanses. Furthermore, this expansion of farmland and shrubberies has resulted in heightened ecosystem fragmentation, particularly notable between 2005 and 2010. Our assessment indicates that artificial ecosystems are gradually transitioning back into natural states, encompassing 8.24% of the total area, chiefly attributed to the expanding shrubbery regions. Additionally, in-depth scrutiny of the impacts of climatic factors on ecosystem structure unveiled that moisture exerts the most pronounced influence on ecosystem patterns, followed by air moisture content during the growing season, while temperature exerts a relatively lesser impact. Overall, this study contributes to the realization of SDG 13 (Climate Action) and SDG 15 (Life on Land) by informing conservation efforts and sustainable land management practices in dryland desert riparian ecosystems.