Ecosystem stability is a multifaceted and complex concept. Understanding the distribution pattern of multidimensional ecosystem stability and its drivers is essential for sustainability. However, the understanding of both the scale dependence and the interaction among different levels of drivers is limited. In this study, the evaluation framework for the multidimensional stability of ecosystems in the Yangtze River Economic Belt (YREB) was constructed by fitting Normalized Difference Vegetation Index (NDVI) to temperature, precipitation, and other meteorological factors from the background characteristics and dynamic change process of ecosystems, and utilizing Auto-Regression (ARx) as well as correlation analysis. Consequently, a hierarchical linear model (HLM) was utilized to assess the impact of natural elements at the basin level and socioeconomic elements at the prefecture level on stability under scale effects and interactions. The results showed that the spatial stability of YREB was higher in the southeast and exhibited a discontinuous distribution in the southwest. The ecosystem multidimensional stability score was the first in the Qiantang River Basin (SI = 0.2586), and the lowest score was in the Taihu Lake Basin (SI = 0.14). In addition, natural and socio-economic factors promoted ecosystem stability to different degrees and along different directions, and the scale dependence of drivers at different levels must be considered. At the basin level, increased soil organic carbon content led to increased stability, while the expansion of farmland and built-up land led to a decrease in stability. At the prefecture level, the population dominated the decrease in stability. Nesting the two scales, demographic and economic factors mainly control stability through their influence on land use, particularly farmland and forestland. Overall, understanding multi-level, multi-scale, and multi-indicator drivers is crucial for strengthening ecological protection in the YREB and controlling the farmland expansion and the urbanization rate growth to maintain the ecosystem stability.