The advancement of urbanization has led to a decline in the ecological function and environmental quality of cities, seriously reducing the services and sustainable development capacity of urban ecosystems. The construction of the National Forest Urban Agglomeration of China is conducive to alleviating the ecological and environmental problems brought about by rapid urbanization and promoting sustainable urban development. A time series analysis of ecological network changes can quickly and effectively explore the development and changes of ecological spatial patterns over time. Identifying ecological protection and restoration areas in urban agglomerations is an important way to promote ecosystem restoration and optimize ecological networks. This paper takes the Pearl River Delta forest urban agglomeration as the research area, uses multi-source remote sensing data from 2000 to 2020 (every 5 years), identifies ecological sources based on the morphological spatial pattern analysis (MSPA) method, generates ecological corridors based on the minimum cumulative resistance (MCR) model, constructs a time series ecological network pattern in the Pearl River Delta region, and analyzes the evolution process of the ecological network pattern over time. The results indicate that over time, the core green area in the ecological network pattern of the Pearl River Delta first decreased and then increased, and the complexity of ecological corridors first decreased and then increased. The main reason is that the urbanization process in the early 21st century led to severe ecological fragmentation. Under the promotion of the national forest urban agglomeration construction, the ecological network pattern of the Pearl River Delta was restored in 2015 and 2020. The time series analysis of the ecological network pattern in the Pearl River Delta region of this research confirms the effectiveness of the construction of forest urban agglomerations, providing a scientific reference for the identification of ecological networks and optimization of spatial patterns in forest urban agglomerations.