The synergistic relationship between water, energy, and food faces increasing challenges. Green finance as a policy tool promotes high-quality and efficient development of water, energy, and food subsystems. However, whether it can improve the synergistic relationship of “water–energy–food” (WEF) still needs to be studied. Using the panel data of 38 prefecture-level cities in the Yangtze River Delta (YRD) from 2013 to 2021, and network DEA and panel regression models, we study the impact of green finance on the level of synergy of “water–energy–food”. The results of the study show that green finance can promote the synergy level of “water–energy–food” in the Yangtze River Delta city cluster, which was first inhibited and then promoted from 2013 to 2021. The impacts of green finance on the efficiency of the three subsystems are also characterized by a “U” shape. However, linear impacts show differences, with green finance improving the efficiency of the water subsystem but not the energy and food subsystems. The implementation of China’s national strategies empowers green finance. The digital strategy, the “dual carbon” strategy, and the new urbanization strategy have increased the effectiveness of green finance in contributing to the level of water–energy–food synergy. Regional heterogeneity analysis shows that the promotion effect of green finance mainly exists in non-resource-based cities, non-main grain-producing areas, and non-cities along the South-to-North water diversion route and large cities. Finally, this paper puts forward relevant policy recommendations.