Ecological space management is an important means to maintain regional ecological security and solve the imbalance between regional ecological supply and demand. The classification of ecological space has always been a hot issue in the ecological management and plays an important role in promoting the sustainable development of urban agglomeration. This paper takes the urban agglomeration of Pearl River Delta as an example, based on the policy goals, public preferences, and expert knowledge of urban agglomeration to comprehensively construct the evaluation system. The initial study of the ecological space management zoning was conducted on the basis of the evaluation of the ecological space quality and ecosystem health. The results showed that the ecological space accounted for 82.8% of the area of the urban agglomeration. The quality of the ecological space was good, but the level of the ecosystem health was low. At the urban scale, the ecological space quality of Zhaoqing and Shenzhen was higher, that of Zhuhai and Zhongshan was lower; the ecosystem health of Huizhou and Zhaoqing was higher, that of Foshan and Zhongshan was lower. Integrated with the quality of ecological space and ecosystem health, the ecological space was divided into key protection area, key restoration area, potential restoration area, and ecological conservation area at the regional scale. The key protected areas accounted for 10.1%, which were the regional ecological source areas. The strictest environmental protection system should be implemented, ecological red line and nature protected area should be delimited, strengthen ecological construction and biodiversity protection, also the construction of ecological connectivity should be strengthened to improve the overall regional ecosystem services. The key restoration areas accounted for 21.6%, mainly focusing on ecological restoration, implementation of ecological projects, and promotion of ecological industry. The potential restoration areas account for 13.1%, mainly focusing on protection and natural recovery, comprehensive conservation and protection and improve the quality of ecological space, and focus on improving the function of ecosystem service. The ecological conservation area account for 55.2%, mainly focusing on ecological corridor construction, strengthening the construction of high standard farmland, and protecting the basis of ecological space. Therefore, the production and construction activities should be carried out reasonably. In this paper, the research on the ecological space zoning could facilitate the decision makers to identify and classify the ecological restoration space and the ecological protection space, and could effectively guide the improvement of the land space planning and the regional ecological environment management system.