Urban green innovation plays a crucial role in achieving sustainable urban economic development, and urban economic resilience is an important manifestation of urban economic development. This prese nt study aims to investigate how green innovation contributes to urban economies’ resilience, which is essential for long-term urban agglomeration expansion and sustainable economic development. To decrease subjectivity and achieve comprehensive evaluation, this study first constructs an index system for evaluating green innovation capability on urban economic resilience, which contains 21 indicators in three areas, including innovation input, innovation output, and green innovation foundation, and the performs a scientific evaluation using the TOPSIS method. On this basis, using the Super-SBM model, the green innovation efficiency value of cities in the Yangtze River Delta (YRD) is calculated. Finally, ArcGIS 10.8 software is used to classify the economic resilience of the 26 cities in the YRD city cluster and analyze the spatial layout characteristics of urban economic resilience. The results show that: (1) the decision evaluation model used in this study is stable and effective, and it can effectively address the issues of subjective assessment processes and information redundancy; (2) green innovation capacity has a positive contribution to urban economic resilience, and its contribution is more significant for cities with strong economic strength; and (3) the green innovation capacity of the YRD city cluster is unevenly distributed, with Shanghai, Suzhou, Hangzhou, and Nanjing having high levels of green innovation capacity and strong urban economic resilience, thus forming the core area of cities radiating outward, showing a “core-edge” spatially. Finally, suggestions for improving the overall economic resilience of urban agglomerations are provided.