The Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is one of four major bay areas in the world, and it is an important strategic development area in China. The GBA has strong open, economic, ecological, social, oceanic and systemic characteristics with important research value. The coastal ecosystem is one of the most important ecosystem types in the GBA. Affected by rapid urbanization, there are many problems in the coastal ecosystem of the GBA. These problems have affected the ecological security of land and sea. Besides, coastal ecosystem restoration is one of the important components of the ecological restoration of territory and space. To promote the restoration of the GBA, this paper puts forward the design idea for the restoration of the coastal ecosystems in the GBA. The idea is based on analysis of the main types and characteristics of the coastal zone in the GBA, by analyzing the main problems in the ecological restoration of the current coastal zone, and relying on the system concepts of a community of landscapes, forests, fields, lakes, grasses (sea) and of the coordination of land and sea. Based on the influence of vegetation, wetlands, hydrogeology, human activities, economic development level, industrial development characteristics, and Hong Kong and Macao Special Administrative Regions on the coastal ecosystem of the GBA, the coastal ecosystem zoning, classification and hierarchical restoration planning framework of the GBA is constructed. A new pattern of the coastal ecological zone in the GBA is composed of the core area of the Pearl River Delta, the GBA, the Pearl River Delta Coastal City Group, and the Pearl River Basin. Under this new pattern, the "ten measures" of the coastal ecosystem restoration plan in the GBA are proposed. Taking watershed as the basic unit of ecological restoration and governance, the various factors that affect the balance of coastal ecosystems are classified and sorted out. This will start from the integrity of the ecosystem and the system of the watershed, by insisting on water-land linkage and land-sea coordination. Then, the integrated restoration of the landscape, forest, field, lake and grass (sea) with water as the core is implemented, so as to realize the new goals of the coastal ecosystem restoration plan of the GBA. Moreover, through the optimization of the coastal ecological environment and the maintenance of the ecological balance of the coastal zone in the GBA, the coastal ecological security pattern of the GBA can be improved. Further, the sustainable development and ecological civilization construction of the GBA will be promoted.