After combing the natural ecological space management and control theories at home and abroad, it is concluded that factors such as physical geography, social economy, and land use changes jointly affect the material circulation, energy flow, biological migration and other key ecological processes of the natural ecological space. In the past, management methods for natural environmental symptoms were insufficient to solve the problems of the integrity and complexity of natural ecological spaces, this research puts forward comprehensive multi-disciplinary theories and multiple space control rules, comprehensive management and control of the multiple ecological elements of the entire natural ecological space is the development trend of ecological space management and control. In order to explore the idea of comprehensive management and control of natural ecological space, taking the Guangdong-Hong Kong-Macao Greater Bay Area as an example, it analyzes the characteristics of the natural ecological space in the Greater Bay Area, such as rich ecological elements, diverse ecological patterns, diverse control systems, and complex development interests.At the same time, it analyzes the control measures and characteristics of the major cities in the Guangdong-Hong Kong-Macao Greater Bay Area, and points out that in the context of growth, the following key issues and their causes exist in the management and control of the natural ecological space in the Guangdong-Hong Kong-Macao Greater Bay Area:(1) Extensive guidelines for construction activities and reduced ecological service functions; (2) Inconsistent ecological space classification standards and low efficiency in the use of ecological land; (3) Separation of powers for space management and control, and insufficient ecological management and control; (4) Shared participation mechanism is not yet available perfect and so on. It is pointed out that the natural ecological space in the Guangdong-Hong Kong-Macao Greater Bay Area should be strengthened to enhance the overall protection of the functional value of the natural ecological space; focus on the connection and refinement of multi-dimensional spatial classification; consider the development needs of cities and counties, and reserve flexible growth space to ensure ecological protection and protective utilization are equally important in the natural ecological space. It also discusses in detail the specific ideas for implementing comprehensive management and control from the ecological service functions of the natural ecological space in the Bay Area, the classification of ecological spaces, dynamic management and control indicators, regional coordination and linkage mechanisms, and space management and control rights and interests, so as to promote the enhancement of the control effectiveness of natural ecological space in the Guangdong-Hong Kong-Macao Greater Bay Area.