This paper analyzed the spatial-temporal pattern of the degree of coordination between economic and environmental development in Beijing-Tianjin-Hebei region, Yangtze River Delta and Pearl River Delta from 2006 to 2016 by means of entropy method, Theil index, Markov chain and spatial autocorrelation, and then explored the influencing factors with Tobit model. The results showed that: (1) The degree of coordination between economic and environmental development of the three major urban agglomerations grew continuously from 2006 to 2016. In addition, the differences between the cities gradually narrowed. (2) Path dependence played a role in the evolution of the level of economic and environmental coordination. However, the degree of coordination between economic and environmental development tended to reach a higher level with the passage of time. (3) Cities with higher administrative levels and some developed cities along rivers or the sea continued to be at a higher level of degree of coordination between economic and environmental development. (4) The spatial characteristics of the degree of coordination between economic and environmental development of the three major urban agglomerations had changed from decentralization to agglomeration. (5) Regarding the type of development, the economically developed cities tended to develop simultaneously with the environment. (6) Energy consumption, progress in science and technology, investment in fixed assets, dependence on foreign investment and ownership structure have impacts on the degree of coordination between economic and environmental development of the three urban agglomerations as a whole and each urban agglomeration, but the significant degree of the influence of each factor is different.