The system of protected areas in China has been initially established, but the effectiveness of ecological protection and restoration remains limited. Conducting an evaluation of ecological protection and restoration effectiveness, identifying priority protected areas, and implementing a regional management model are crucial for regional sustainable development. This study focuses on the Yangtze River Delta Urban Agglomeration, integrating multiple dimensions, including ecosystem patterns, quality, function, and social-ecological feedback, to develop a framework for evaluating ecological protection and restoration effectiveness. Furthermore, we identified key ecological areas and the spatial distribution of priority protected areas. The results showed that: Significant differences in the ecological protection and restoration effectiveness of protected areas across various indicators. Overall, from 2018 to 2022 indicators such as landscape connectivity (+2.17%), vegetation cover (+9.38%), biodiversity (+5%), soil conservation capacity (+4.91%), and carbon sequestration and oxygen release function (+4.46%) achieved an excellent level, while public satisfaction (+2.56%) reached a good level. However, indicators such as important ecological land area (-1.04%), air quality (-16.85%), water conservation capacity (-16.17%), and human footprint (+7.83%) showed a poor level. A total of 21 priority protected areas were identified in the study area, mainly distributed in the Taihu Lake Basin, Northern Zhejiang, and Northern Anhui. Based on the research results, a regional management model of "3-Core Dynamic (3CD)" was proposed, comprising zonal control, node linkage, and dynamic optimization. This study provides scientific references for regional ecological protection, restoration, and sustainable development.