Coordinating ecological network patterns with the urban network patterns is crucial for sustainable development in urban agglomerations. The bay area urban agglomerations, with their unique geographical advantages and economic vitality, have become the core unit of regional development, but the synergy between ecological and urban development is increasingly critical. Taking the Guangdong-Hong Kong-Macao Greater Bay Area as an example, by comprehensively applying methods such as morphological spatial pattern analysis, landscape pattern indices, and the least cumulative resistance model to determine ecological sources and economic and social sources, identify ecological corridors and traffic corridors, construct the ecological and urban dual network pattern of the bay area urban agglomeration region, explore the spatial relationship and interference of the dual network pattern, and finally propose suggestions for cross-regional ecological synergy in the bay area urban agglomeration. The results showed that (1) The study area contains 30 ecological sources spanning 21205.0 km² and 422 socioeconomic sources spanning 7629.35 km².. The total area of ecological and transportation corridors are 8506.98 km²and 4562.11 km²respectively, together forming an outer ring-shaped ecological barrier and an internal cyclical network for urban development around the study area. (2) The study area features 1011 key ecological points and 7527 ecological disturbance points, offering opportunities for targeted restoration and protection to enhance ecological connectivity significantly. (3) Three types of ecological synergy in the study area were identified based on source, watershed and coastal wetland. A framework for constructing a cross-regional ecological synergy model for urban agglomerations was proposed.