The Guangdong-Hong Kong-Macao Greater Bay Area (hereafter the Greater Bay Area) is a high-intensity development area in China's coastal zone, facing the pressure of serious damage to coastal ecosystem and low ecological environment quality. It is necessary to protect and restore the coastal ecosystem in the development of the Greater Bay Area. Based on analysis of the present situations and problems of the Greater Bay Area, we provide strategies to protect and restore the Greater Bay Area's coastal ecosystems and put forward five aspects to develop the planning system of protecting and restoring the Greater Bay Area ecosystem: 1) to restore the marine biologically survival environment by land and sea pollution control; 2) to strengthen the protection of coastal ecology through the protection of natural coastlines, reconstruction and standardization of protected area system, and protection of the habitats of rare and endangered species; 3) to construct ecological barrier through ecological restoration of coastlines, coastal wetland ecosystems such as the degraded mangroves, coral reefs, seaweed beds and damaged islands; 4) to promote the synergy and efficiency of ecological disaster reduction through ecological transformation and construction of seawalls and coastal shelter forest systems, as well as the demonstration of the integrated disaster prevention system; 5) to build a smart coastal zone management service platform to ensure the healthy development of the community of a shared maritime destiny. This study proposes strategies and suggestions for ecological protection and restoration of the coastal zone in the Greater Bay Area in order to provide references for ecological development and environmental protection.