With the rapid urbanization in China, ecosystems and relevant ecological issues of large metropolitan areas have increasingly become a source of concern. To promote ecological protection, restoration, and refined management, it is necessary to analyze and identify regional ecological security and restoration patterns. Here, we used the Pearl River Delta region as the study area. First, six key ecosystem services were quantitatively modeled and mapped based on the InVEST ecological tool. Some parts with high ecosystem services were identified as ecological sources according to the self-organization feature map (SOFM) neural network model. Second, a resistance surface of ecological flow was developed by integrating the factors of surface land cover, landscape connectivity, and human activities. Subsequently, the minimum cumulative path model was used to identify the basic trend of the regional ecological corridor and the spatial distribution of ecological nodes. Based on this analysis, the gravity model was applied to classify the importance of ecological zones and ecological corridors according to the correlation between ecological sources and extract ecological obstacle points. Based on the above analysis, 36 ecological sources, mainly forest land, were identified, which accounted for approximately 29.56% of the total area. In addition, based on the least resistance path model, we identified 141 key ecological corridors (1900 km), 10 ecological nodes connected with ecological flow, and 2776 km² high-priority ecological restoration area. Finally, the key ecological sources and their radiating areas were integrated to form five ecological zones in the northeast, northwest, southeast, west, and south, according to the importance level of the ecological corridors determined by the gravity model. Therefore, this study proposed a regional ecological security and restoration pattern of the Pearl River delta, which took ecological source as the core, ecological corridor as the main axis, ecological node as the connecting point, and ecological obstacle point as the restoration area. Corresponding ecological restoration and management measures were also put forward for various ecological elements, which would be beneficial for solving regional ecological issues in large metropolitan areas.