Abstract: Yangtze River Delta region is not only a strategic place for ecological civilization construction in China, but also a core demonstration area for the construction of terrestrial and marine ecological security framework and realization of sustainable development. In order to evaluate the security framework of marine ecological space in Yangtze River Delta, various types of existing Marine Protected Areas (MPAs) were investigated through review and evaluation of the performance of MPAs in the region. Three key challenges faced by the region are: the target species/habitats for protection are difficult to be effectively protected, the sustainable development of the region is threatened by multiple marine ecological disasters, and the survival status and habitat conditions of some endangered marine species are not optimistic. The authors suggest that the region needs to construct a scientific system of MPAs to improve the network connectivity of MPAs and build an integrated management system.