The coupling effect of green innovation participants, elements, and environments directly reflects the operation and evolution of a green innovation ecosystem. This paper studies the spatial organization mode of green innovation ecosystems and the structural evolution and self-organization mode of their associated networks under this coupling effect. By selecting relevant data from 286 cities in China from 2010 to 2021, the green innovation ecosystem coupling coordination index (GIECCI) is calculated using a coupling coordination model. The calculation result is used as a weight to modify a gravity model to construct an innovation ecological network. After analyzing the calculation results, the findings are as follows. (1) The polarization effect of the GIECCI is significantly alleviated, presenting a quantitative structure close to the normal distribution; However, the existence of the Matthew effect trap leads to great resistance to green innovation in some cities. (2) Cities with the same or a similar GIECCI are more likely to form agglomerations, including mature, cross-distribution, and budding agglomeration models. (3) The connectivity status of urban nodes significantly varies, and the mismatch between connectivity symmetry and the total strength of green innovation gravity is widespread. These findings may provide a reference for government departments to plan the layout of green innovation industries and choose sustainable innovation strategies for enterprises.