The improvement of port cluster eco-efficiency is of great significance to constructing a world-class shipping hub and the high-quality development of regional economy. This study adopts the Super-EBM (Super-efficiency Epsilon-Based Measure) model to evaluate the eco-efficiency of the Yangtze River Delta port cluster in China, and the GML (Global Malmquist-Luenberger) index, spatial hot spot analysis, gravity center migration model, and the Theil index are combined to reveal the spatial-temporal evolution. The results show that the average eco-efficiency of the Yangtze River Delta port cluster is 0.686, with 55.6% of the ports being below the average, which is directly related to the low scale efficiency. Mainly driven by technical efficiency improvement, the overall eco-efficiency has a growth rate of 8.7% from 2010 to 2019. Moreover, considerable spatial divergence has formed in the port cluster, and the eco-efficiency gravity center has always been in the south of Jiangsu. The overall eco-efficiency gap has widened by 19.92%, and the gap within the region, particularly within Zhejiang, is the major source. To improve the overall eco-efficiency of the port cluster, policymakers should strengthen the technological spillover of ecologically efficient ports in clean production and mechanism reform, while optimizing the resource consolidation system of ports with relatively low eco-efficiency.