Abstract: The continuous advancement of urbanization and industrialization has greatly threatened the natural capital and its sustainable utilization in urban agglomeration. In order to clarify the characteristics of natural capital sustainability changes during the construction process of urban agglomerations, taking the Yangtze River Delta urban agglomerations as an example, two-dimensional and three-dimensional ecological footprint models were applied to analyze the change of ecological footprint, ecological pressure index (EPI) and ecological economic coordination index (EECI), the natural capital stock consumption and natural capital flow occupancy, as well as the influencing factors and its related mechanisms, by adding the water resources account to the adapted ecological footprint model to reflect the water resource potential and demand in this area. The results showed that during the study period, the per capita ecological footprint and ecological carrying capacity of the Yangtze River Delta urban agglomeration were 4.46 hm²/person and 1.59 hm²/person, respectively; and the average per capita ecological deficit was 2.87 hm²/person; however, the ecological footprint per unit GDP continued to decline, indicating that the utilization rate of resources continued to rise. From 2005 to 2019, the EPI value of the Yangtze River Delta urban agglomeration increased from 2.48 to 3.25, and the EECI value fell from 1.30 to 1.25. Based on the revised three-dimensional ecological footprint model, it was found that the use of natural capital stock in the Yangtze River Delta urban agglomeration was increasing, and it had a significant inhibitory effect on the renewal of natural capital flows, and the consumption of natural capital stock was 2.26 times of capital flow in 2019, with the resource consumption occupied. The impact factors analysis showed that the industrial output value, total energy consumption, construction land area and urbanization rate played positive roles in promoting the ecological footprint and exerted greater pressure on the sustainability of natural capital. The relationships among the ecological pressure level, ecological environmental and economic development of the Yangtze River Delta urban agglomeration were quantitatively analyzed to provide a scientific basis and decision support for improving the ecological security and sustainable development of urban agglomerations.