Rapid urbanization has led to some problems in China, such as local ecological degradation, massive crowding of ecological space and so on, resulting in serious threats to ecological security, especially in the eastern coastal areas. Identifying ecological networks can promote sustainable development while maintaining the integrity and stability of the ecosystem, which is of great significance for ensuring the ecological security of fragile ecosystems and regions with a high degree of urbanization. Previous studies have seldom considered the possible impact of temporal and spatial changes on habitat quality. The related studies on the determination of the ecological corridor width are few, the methods are not yet mature, and the accuracy and spatial accuracy are in doubt. Taking Guangdong-Hong Kong-Macao Greater Bay Area as the research object, we analyzed the spatio-temporal evolution characteristics of habitat quality in 2000, 2010, and 2020 using InVEST model. In the identification of ecological network, we selected the ecological source based on the identification of landscape elements based on morphological spatial pattern analysis, and classified the ecological source level according to the long-term series of landscape connectivity and habitat quality assessment. Then, based on the circuit theory method, we extracted the spatial location and width of the ecological corridor, identified the ecological "pinch points" and ecological barriers, and formed the ecological network of the Guangdong-Hong Kong-Macao Greater Bay Area. Finally, we discussed the optimization strategy of ecological network and identified key areas of priority conservation and restoration. The results showed that:(1) the habitat quality of the study area presented an overall downward trend from 2000 to 2020, and showed a spatial pattern trend decreasing from the center to the edge. (2) there were 117 ecological sources in the study area, mainly distributed in the hilly and mountainous areas around the periphery, while sparsely distributed in the central area, forming a semi-surrounded situation, including 7 primary ecological sources, 13 secondary ecological sources, and 97 tertiary ecological sources, with a total area of 2597.72 km², accounting for 46.39% of the study area. (3) there were 243 ecological corridors in the study area, including 104 primary corridors and 139 secondary corridors, with a total length of 1273.84 km. (4) there were 88 ecological "pinch points" and 188 ecological barriers in the study area, which were key areas for priority protection and restoration. The method based on habitat quality assessment has strong applicability for the construction of the Guangdong-Hong Kong-Macao Greater Bay Area ecological networks, to provide reference and support for strengthening ecological space management, optimizing the land spatial structure and ecological restoration.