This study focuses on the lower reaches of the Heihe river in Northwest China’s arid region, utilizing MOD13 Q1-NDVI data from 2000 to 2022, complemented by concurrent temperature (Tem) and precipitation (Pre) records, to investigate the spatiotemporal dynamics of fractional vegetation cover (FVC) and its response mechanisms in the context of climate change. The findings reveal that: 1) The FVC in the lower Heihe river region exhibits an overall trend of slow, fluctuating improvement, indicating a gradual recovery. However, the FVC remains relatively low, with the core oasis areas displaying weak ecological stability. These regions are highly susceptible to the impacts of climate change and human activities, thus exhibiting significant ecological fragility. 2) Climate change in the lower Heihe river region is influenced by global trends while it exhibits distinct local characteristics. The region has experienced a pronounced warming trend with notable fluctuations in Tem increases. Meanwhile, Pre has shown a slight decline, characterized by highly unstable interannual variability. The increasing aridity of the climate has further exacerbated the risk of vegetation degradation. 3) The relationship between FVC changes and Tem or Pre is weakly correlated. These climatic factors have influence on FVC, but they are not the primary drivers. FVC is also significantly affected and constrained by other factors such as surface water availability, groundwater levels, and soil salinity.