The rapid growth of the marine economy has provided a strong impetus for the economic development of the Yangtze River Delta region, but it has also posed serious challenges to the ecological environment of the marine watersheds in which it is located. To investigate how to promote the sustainable development of the marine economy in the Yangtze River Delta region, this study used relevant statistical data from 2009 to 2019, combined with four factors—marine economy, marine resources, ecological environment, and scientific and technological innovation—to build an evaluation index system for the sustainable development of the marine economy and employed the entropy value method to conduct a deeper investigation. It was found that there are problems in the sustainable development of the Yangtze River Delta marine economy, such as imperfect marine industry structure, significant differences in resource allocation, insufficient support capacity of marine science and technology innovation, and insufficient ecological environmental protection. Therefore, the study suggests promoting regional collaboration in the Yangtze River Delta, improving technological innovation, and enhancing environmental protection to support the sustainable development of the regional marine economy.