Sustainable development evaluation is a complicated component of system engineering. In ecological economics, capital stock stability is used to evaluate sustainability; however, previous studies have used a single indicator to evaluate natural capital, which cannot reflect the sustainability of regional development. Here, we studied the theories of ecological economics, drew lessons from ecological efficiency and carbon intensity concepts, and introduce the concepts of capital flow and capital stock to analyze the utilization efficiency of natural capital in the Yangtze River Delta. A spatial error model was used to study the influencing factors and determine the sustainable development from 2000 to 2019. The results showed that: (1) From 2000 to 2014, natural capital in the Yangtze River Delta region was intensified and had low efficiency. From 2014 to 2019, capital use gradually balanced and showed sustainable development. (2) Natural capital utilization efficiency was affected by resource conditions, industrial structure, regional location. The higher the tertiary industry proportion, the closer the location to the central city, the better the economic development foundation, the higher the natural capital utilization efficiency, and the better the sustainable development. (3) Natural capital utilization change was due to the regulatory role of the government.The One Belt One Road strategy and urban integration strategy proposed by the Chinese government have greatly changed the market structure.