Abstract: As the integration point of “innovation-driven” and “green development”, green innovation efficiency has become the key to promoting high-quality development in Yangtze River Economic Zone (YREZ). This study empirically analyzed the spatial correlation network structure and driving factors of green innovation efficiency from the perspective of social network analysis. The study finds that the overflow channels and mutual relation between provinces increase yearly, so does the density of spatial correlation networks. Green innovation efficiency in all provinces are influenced by other regions and the overall spatial network in this basin, the hierarchical spatial structure is gradually broken down, and the network structure becomes increasingly stable. However, synergistic development of green innovation efficiency in different regions still needs to be improved. The formation of “plates” in the network breaks the traditional administrative boundary, the provinces changed from discrete to united gradually, and the diffusion radiation made the provinces in the basin form a cluster development. The transmission mechanism of correlation network has obvious gradient overflow characteristics, meanwhile, the “Matthew effect” is obvious. In addition, constrained by the large gap between economic development model and green innovation environment in this basin, the willingness and motivation of trans-regional innovation cooperation is weakened, and flow of elements of green innovation efficiency is blocked, resulting in a reduced correlation probability among those provinces and municipalities. Therefore, based on their roles in the spatial correlation network, the provinces and municipalities in this basin should grasp the overall spatial transmission mechanism of the improvement of green innovation efficiency, form an “attribute-relationship”-driven development approach, narrow down the difference in green innovation environment, and promote factors flow across regions to realize the green and coordinated development of the basin’s economy.