Abstract: A comprehensive evaluation index system for the green innovation capacity of cities in the Yangtze River Delta region was established based on three aspects of green innovation input, green innovation output, and green innovation environment. The global entropy weight method was used to measure the green innovation capacity of 41 prefecture level cities in the region from 2010 to 2021. Based on the improved gravity model, a green innovation network of cities in the Yangtze River Delta region was constructed. The social network analysis method was used to explore the network characteristics of the spatial correlation of green innovation in cities in the Yangtze River Delta region from three aspects: overall, individual, and local. The quadratic assignment program (QAP) regression analysis method was used to explore its influencing factors. The results indicate that from 2010 to 2021, the spatial correlation of green innovation among cities in the Yangtze River Delta region increases year by year, but there is still room for improvement overall. At the same time, there are regional differences, and the development trend in the eastern region is better than that in the western region. The core cities serve as bridges and intermediaries, mainly concentrated in the eastern and central regions, with some cities being “net beneficiaries” and unable to actively establish connections with other cities. The northern, southern, and southern regions of Anhui are mostly peripheral cities with weak external connections and an uneven trend in urban green innovation development. Differences in higher education level, scale of financial development, degree of openness to the outside world, and level of informatization are the main factors affecting the spatial correlation of green innovation networks in the Yangtze River Delta cities. To promote high-quality development of green innovation in the Yangtze River Delta region, the radiation range of core cities should be expanded to drive the development of peripheral cities; Build a central city within the third and fourth subgroups, serving as a bridge and intermediary for communication with the outside world; Narrowing the gap in regional financial development scale, improving the infrastructure for cross city cooperation, and engaging in knowledge and technology exchange, interaction, and resource sharing.