The quality of Marine ecological environment is one of the necessary conditions for building a world-class bay area. The ecological environment in the coastal waters of Guangdong-Hong Kong-Macao Greater Bay Area is seriously polluted, it is urgently needed for three places to strengthen coordinated Marine ecological and environmental management. Under the guidance of outline development plan for the Greater Bay Area and with the goal of building a Marine ecological civilization in the Greater Bay Area, the coordination mechanism of administrative management and the standard system for Marine ecological environmental protection should be improved，land and sea overall planning should be used for Marine ecological environment protection.