Abstract: In the green development era, the construction of a high-level regional green innovation network can help to promote the high-quality development of cities and regions. Based on the co-application data of green invention patents, the intercity collaborative green innovation networks of urban agglomerations in the middle and lower Yangtze River were constructed from 2016 to 2020. This study comparatively explored the network structure characteristics and the driving forces of green innovation network of urban agglomeration in the study area through network descriptive analysis and the Exponential Random Graph Model. Results showed that: (1) the green innovation network of the Yangtze River Delta urban agglomeration was more densely developed with strong integrity and accessibility, and presented a multi-center spatial structure with Shanghai, Nanjing and Hangzhou as the core. The green innovation network of the urban agglomeration in the middle reaches of the Yangtze River was relatively sparse with significant core-edge structural characteristics, weak integrality and accessibility, and presented the dual-core radial pattern with Wuhan and Changsha as the core. (2) The municipalities or capital cities of the Yangtze River Delta urban agglomeration had stronger organizational function, but weaker intermediary function, compared with the weak organizational function and strong intermediary function of the municipalities of the urban agglomeration in the middle reaches of the Yangtze River. (3) The green innovation networks of urban agglomerations in the middle and lower Yangtze River were both characterized by self-organized growth. Geographic proximity, institutional proximity and industry similarity influenced the formation of the two networks in the same direction, but to different degrees. The phenomenon that cities at high levels of economic development were more likely to cooperate with each other only occurred in the green innovation network of the Yangtze River Delta urban agglomeration. The structure and driving forces of green innovation networks of the two urban agglomerations were quite different. It is, therefore, crucial to promote the integrated development of regional green innovation according to the local conditions. Yangtze River Delta urban agglomeration should accelerate the integration of Anhui cities. Urban agglomeration in the middle reaches of the Yangtze River should break the administrative barriers as the primary task.