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Accurate assessment of the sustainable development level is crucial to providing reasonable and effective management recommendations. However, analysis with a single scale can only reflect the sustainable status at a specific level. In this study, a multi-scale analysis of sustainability was conducted via the three-dimensional Ecological Footprint (EF) model in the Yangtze River Delta (YRD). Moreover, driving factors of sustainability were analyzed using the Multi-scale Geographically Weighted Regression model (MGWR). The conclusions include: (1) the development of YRD showed an unsustainable trend from 2014 to 2021, with per capita EF decreasing from 5.769 ha/cap to 5.283 ha/cap. The provincial sustainability is ranked as follows, from being the most sustainable to the least: Anhui Province > Jiangsu Province > Zhejiang Province > Shanghai City. (2) Based on dual indicators of EF depth and size, 41 cities were categorized into nine groups. The dominant type is always Medium size-Low depth (ML) and High size-Low depth (HL) type cities from 2014 to 2021. From the perspective of city scale, the sustainability of five cities weakened, while seven cities showed improvements. (3) Output value of primary industry (OVPI) and population (POP) were always the dominant factors affecting EF, but showed positive and negative correlations respectively. OVPI changes from north-south symmetric type to central symmetric type, while POP changes from central symmetric type to north-south symmetric type. This paper aims to comprehensively assess the sustainable development status from agglomeration-province-city perspectives, and its findings can provide a reference for similar regions with unbalanced development status between ecology and production. • The sustainability of the world-class urban agglomeration was assessed via the three-dimensional ecological footprint model. • More comprehensive and accurate analysis results based on multi-scale analysis. • The four patterns of influencing mechanism are revealed based on the MGWR model. • The combination analysis of dual indicators was adopted to classify the sustainability of 41 cities. [ABSTRACT FROM AUTHOR]