This study puts forward a logical framework for green innovation network analysis, which includes a spatial dimension, a relational dimension, and a systems dimension. Here, we put forward some basic research ideas concerning the optimization and regulation of green innovation networks in terms of the systems dimension and we investigate the micro-dynamic mechanisms of green innovation network expansion using a spatial econometric model. Our main research results are as follows: The efficiency of green innovation in the Yangtze River Economic Belt has improved significantly, however, the gap between cities has gradually increased, and a problem of efficiency regression has emerged. The green innovation network has changed from the primary stage dominated by Edge Network to the rapid growth stage dominated by Supporting Network, and formed a complex network pattern with diversified hierarchical structure. Node symmetry is helpful in forming more extroverted connections and promoting the expansion of green innovation networks. Node proximity and connection symmetry inhibit the growth and development of networks, and knowledge flow cooperation networks can accelerate the evolution of green innovation networks. Finally, this paper holds that we should combine the actual development needs, emphasize the basic principles of differentiated development, and construct the development pattern of regional collaborative innovation. This can also provide a theoretical reference for enriching our understanding of green innovation networks while narrowing the gap between cities.