Enhancing the effectiveness of urban green innovation is a powerful strategy for advancing urban sustainability. A strong urban innovation ecosystem is a crucial building block for advancing urban green innovation’s effectiveness. We use the fsQCA method to investigate the pathways and models of innovation ecosystems to promote the green innovation efficiency of cities from a histological perspective, using 71 innovative cities in China as cases. This method is based on the DEA-SBM model to measure the green innovation efficiency of cities and the Necessary Conditions Analysis. According to our analysis, individual innovation factors are not required to increase urban green innovation efficiency. But cities with good openness can attract creative forces and foster open innovation, which is essential for producing high levels of green innovation efficiency in cities. The innovation subject-balanced development model, the innovation environment-innovation asset dual drive model, and the innovation subject-open drive model have all been identified as additional models to support urban innovation efficiency. Finally, we discovered that it is not possible to increase the efficiency of green innovation in the city when each innovation factor in the city is performing poorly, and when there is also a lack of innovation subject and system openness. This study attempts to offer fresh theoretical angles and a variety of urban low-carbon development pathways.