Abstract: As an important evaluation index of ecosystem services, carbon storage and its change researches are an important topic of global terrestrial ecosystem carbon cycle and tackling climate change in recent years. Due to increased human activity interference and climate change, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), one of the most important economic core areas in China, is undergoing rapid changes and facing huge ecological environment pressure. With the InVEST model, this research quantitatively evaluates the carbon storage of GBA in 2005, 2010, 2015 and 2018 respectively, and analyzes the spatio-temporal evolution and spatial differences. The results show that: 1) In 2005, 2010, 2015 and 2018, the carbon storage of GBA was 202.41×106 t, 200.87×106 t, 199.99×106 t and 200.10×106 t respectively, and the change of total carbon storage showed a trend of decreasing first and then increasing; 2) A large amount of forest land and cultivated land was occupied for construction purpose, the total carbon storage of GBA decreased by 1.14%, and the annual loss rate stood at 0.09%; 3) From 2015 to 2018, the carbon sequestration in GBA turned from negative to positive, indicating that the government’s ecological protection policies have achieved initial results in recent years. Under the development goal of the low-carbon bay area, the carbon storage and carbon sequestration capacity of GBA would be greatly improved by protecting cultivated areas and forest land and vigorously promoting the project of green enhancement and carbon sink project.