With the rapid economic development，the Guangdong-Hong Kong-Macao Greater Bay Area is facing the serious eco-environment problem，such as water pollution，air pollution and soil pollution. The good eco-environment is very important to promote the sustainable and high quality development of the Guangdong-Hong Kong-Macao Greater Bay Area. It is found that the water and air environment of Guangdong-Hong Kong-Macao Greater Bay Area is worse than that of world-class Bay areas，but slightly better than that of major domestic urban agglomerations. Within the Guangdong-Hong Kong-Macao Bay area，the water pollution on the East Bank of the Pearl River is more serious，and the air pollution on the West Bank of the Pearl River is more serious. Based on the data analysis of the Guangdong-Hong Kong-Macao Greater Bay Area from 2006 to 2018，the quality of urban social development in Guangdong-Hong Kong-Macao Bay Area is divided into two levels. The gap between cities is mainly reflected in the level of economic development，while the difference in the level of eco-environment protection is small. The interactive development between economy and eco-environment protection of each city gradually strengthens to the benign coupling，and develops in an orderly direction. On the above conclusion，this paper puts forward some suggestions to further promote the development of eco-environment protection in the Guangdong-Hong Kong-Macao Greater Bay Area.