Exploring the interactive relationship between institutional cyberspace and functional geographical space is conducive to promoting regional collaborative development. Taking the Guangdong-Hong Kong-Macao Great Bay Area (GBA) as the research object, this study analyzed the evolution characteristics of regional cooperation and urban factor agglomeration based on social network analysis and comprehensive evaluation. Furthermore, it described the interaction characteristics of urban factor agglomeration and regional cooperation by using exploratory spatial data analysis, ridge regression, and other methods. The main results showed that: 1 The regional cooperation network was becoming intricate, and the cooperation nodes took Hong Kong and Shenzhen as the preferred attachment objects in the GBA. On the whole, the eastern bank area had more density than the western bank area along the Pearl River, and there was homogeneity in the cooperation field in the western bank area and marginalization of Zhaoqing and Huizhou. 2 The level of urban factor agglomeration was relatively high, forming a population agglomeration area, an economic growth pole, and an industrial peak. The eastern bank area had more development strength than the western bank area along the Pearl River. There were features of interconnection between adjacent cities and the blurring of administrative boundaries. 3 Regional cooperation had a local overflow effect on urban factor agglomeration. Furthermore, the overall regression showed that urban factor agglomeration had both positive and negative effects on regional cooperation. Specifically, population and capital factor agglomeration became the main driving force to promote regional cooperation. Communal facilities agglomeration had a negative effect on regional cooperation by contrast. 4 The local regression showed that the positive effect of economic cooperation on the urban factor agglomeration became more significant. Ultimately, urban factor agglomeration would promote the network structure under shared network governance, otherwise, it would be dispersed to form a core-periphery structure under leadership network governance. Under the background of regional factor agglomeration and unbalanced development, urban relationships were facing reconstruction in the GBA. By means of the Hong Kong-Zhuhai-Macao Bridge and the flow of elements, the GBA should focus on the integration of population, capital, land, infrastructure, and other elements with economic development, social progress, and institutional exchange. Marginal cities, such as Zhaoqing and Huizhou, should give full play to their comparative advantages and encourage regional governance to lean on a shared network structure. In addition, the GBA should tap the internal potential and form collection and scale effects among cities, so as to jointly resist external risks. [ABSTRACT FROM AUTHOR]