Background As one of the most dynamic areas in the world for economic activities, the carbon stock of the Guangdong-Hong Kong-Macao Great Bay Area is affected by multiple factors including land use types, and the study of the characteristics of spatial and temporal changes in carbon storage and its driving factors in the Greater Bay Area is of great significance for the sustainable development of the regional soil conservation, economy and ecological environmental protection.

Methods This study qualitatively and quantitatively evaluated the carbon storage in the Greater Bay Area from 2000 to 2020 based on InVEST model, analyzed its spatial and temporal variations. Then, correlation analysis was used to explore the relationship of carbon storage with normalized difference vegetation index (NDVI), average annual precipitation (Prec), average annual temperature (Temp), night light data (NL), total population (POP), population density (PD), gross domestic product (GDP), gross domestic product per capital (GCP), and urbanization rate (UR).

Results 1) The most obvious land use changes in the Greater Bay Area from 2000 to 2020 were cropland (−22.24%) and construction land (+53.66%), while the rest of the land use types have not changed much. 2) The high value areas of carbon storage in the Greater Bay Area were concentrated in the hilly and tableland areas in the northwest, southeast and west, while the carbon storge on both sides of the Pearl River estuary showed low levels. Among all the cities in the Greater Bay Area, only Shenzhen and Zhaoqing had positive carbon storage growth, while the rest of the cities have negative growth. 3) The carbon storage in the Greater Bay Area was significantly negatively correlated with POP, PD, UR, and NL (R < 0, P < 0.05), and showed a significant positive correlation with NDVI (R > 0, P < 0.05).

Conclusions The massive influx of migrant populations, rapid economic growth, and swift urban development in the Greater Bay Area have led to significant encroachment on forested and agricultural lands, resulting in a negative growth in regional carbon stocks. Therefore, the establishment of ecological protection red lines, cultivated land protection red lines, and urban development boundaries is crucial for enhancing the carbon sequestration capacity of the region, as well as strengthening the resilience of its ecosystems and the functions of soil and water conservation.