The spatial structure inherently reflects a region's pattern and developmental processes. Understanding the rationality behind this structure and identifying optimization directions are pivotal for macro-level regulation of regional development and collaborative efforts. This study initiates a discussion on the composition and optimization mechanisms inherent in spatial structures. Adopting a spatial network perspective, we interpret the interaction dynamics within regional morphological structures as the consumption of resources through flows. We transform structural optimization into an equilibrium matching process of resources and establish a quantitative research framework that integrates network modeling, structural issue identification, and optimization strategies. Then, we selected the Guangdong-Hong Kong-Macao Greater Bay Area as our empirical subject, and obtained three important results: (1) Before optimization, we identified structural spatial imbalance characteristics; (2) We explored the evolutionary trend of optimization and delineated four main optimization stages; (3) The spatial structure of the region was improved, and significant benefits in equilibrium and resource utilization was achieved. Finally, we discussed the feasibility of the framework and the necessity to integrate policy networks, hoping to assist regional managers in macro-governance and enhance the rationality of regional planning and coordination.