It is of great significance to monitor the variations of fractional vegetation cover (FVC) and assess the impact of large-scale geological sets, especially the active tectonics on vegetation variability for a deep understanding of the spatio-temporal pattern of ecosystem. The Inner Mongolia section of the Yellow River Basin belongs to arid and semi-arid areas, where the vegetation is mostly dependent on groundwater and the active tectonics are frequent, so it is an ideal area for understanding the azonal characteristics of vegetation. Based on MODIS NDVI (Normalized Difference Vegetation Index), meteorological and land-use data, this paper analyzed the spatio-temporal variation and stability of FVC in the Yellow River Basin (Inner Mongolia section) from 2000 to 2018 and further explored the reasons for strip distribution of vegetation. The results showed an increasing trend of FVC in the past 20 years. The increase in rainfall was the main reason for the increased FVC in the Dahei River Basin, Hun River Basin, and Ten Kongdui Basin. The Three-North Shelterbelt Project contributed to increased FVC in the desert regions. Dahei River Basin and Hun River Basin had better water conditions and rich biodiversity with high FVC, helping to resist external disturbances. In contrast, the Ten Kongdui areas and deserts with lower FVC and fragile ecosystems were more sensitive to climate fluctuations. Hetao irrigation area is dominated by human activities, characterized by weak sensitivity of FVC to climate change. The vegetation grows along the groundwater overflow belt in the piedmont zone of Hetao. It increases as the groundwater storage increases. Over the piedmont transition zone, the soil layer is thin and its water storage capacity is poor due to large surface height difference caused by neotectonic movement, manifested as the high fluctuation of FVC. The vegetation along the mainstream of the Yellow River reduced due to land-use change and its stability was poor under the disturbance of river oscillation and channel migration. At the boundary between the Hetao Basin and the Ordos platform, groundwater tends to infiltrate along the permeable faults forced by seismic activities, which makes it difficult to maintain shallow water and stable recharge conditions, thus resulting in a significant linear decrease of FVC and poor stability. This study highlights the role of macroscopic geological background (i.e., hydrogeological conditions and surface processes) on vegetation pattern and has a deep insight into the azonal characteristics of vegetation, which provides a better scientific basis for similar studies.