Abstract: Based on the panel data of cities in urban agglomeration in the middle reaches of the Yangtze River from 2010 to 2022, this study explored the characteristics of spatio-temporal distribution and influencing factors of green technology innovation. The methods of Kernel density estimation, Dagum’s Gini coefficient, spatial autocorrelation analysis, social network analysis and spatial Durbin model were used in this study. The results showed that: (1) The levels of green technology innovation in urban agglomeration in the middle reaches of the Yangtze River and the three regions showed a decreasing growth rate. There was heterogeneity in their levels of change in absolute differences and polarization characteristics. (2) The overall differences maintained at a high level, with hypervariable density and inter-regional differences being the main sources. (3) The spatial distribution was uneven, and most cities were concentrated in low-value or lower-value regions, and the core-edge characteristic was obvious. The type of spatial agglomeration was primarily characterized by low-low agglomeration, with a relatively stable trend of agglomeration. (4) The scale of cooperation network had developed significantly, and the accessibility and connectivity had increased significantly. A leading rise was indicated in the core cities of Wuhan and Changsha, and a rise in Nanchang and Zhuzhou cities, which formed a situation of “multi-core leading + multi-point support”. (5) The level of economic development, environmental regulation, innovation support and financial level promoted green technology innovation in local cities, while the dependence on foreign investment and the degree of opening up to the outside world showed an inhibiting effect. The industrial structure based on the tertiary industry promoted the neighboring cities, while the degree of opening up to the outside world had an inhibiting effect.