Super large-sized cities and very large-sized cities (“mega-cities” for short) have become the backbone of China's socio-economic development, but they also face outstanding challenges of "urban diseases" due to their high concentration. In comparison to their foreign counterparts, China's mega-cities possess unique characteristics such as rapid growth, high population density, and large numbers of residents. They naturally have the attributes of metropolitan areas due to an administrative management system of an urban system within city territory. Promoting coordinated spatial governance of mega-cities via spatial organization of metropolitan areas not only helps mega-cities better allocate resources at a larger scope and helps expedite the transformation of development patterns, but is also crucial for better implementing new-type urbanization strategies. In response to the issues in China’s previous research and practices related to mega-cities and metropolitan areas, leveraging the “Critical Technology for Spatial Optimization of Metropolitan Areas of City Clusters” of the national key R&D plan in the “14th Five-year Plan” period, we have employed a scientific approach that combines data and models to propose spatial governance strategies. These strategies encompass both the overall metropolitan area level and the cross-border regional level. Our primary focus lies in optimizing the spatial layout of the “three domains” – ecological space, production space, and living space, facilitating functional dispersal, enhancing spatial patterns, adjusting land use structures and spatial resource allocation, coordinating rail transit and the organization of functions along transit lines, and innovating service management for improvement of administrative efficiency. Through the implementation of these diverse measures, we aim to establish a comprehensive composite collaborative system.