With 27 cities in the Yangtze River Delta urban agglomeration as the research object, and based on static and dynamic perspectives, the super-efficiency SBM model and Malmquist index are used for a measurement and analysis of their green innovation efficiency from 2013 to 2018. The empirical results show that there is a great diversity among the cities in the green innovation efficiency of the Yangtze River Delta urban agglomeration, with a descending order of the average green innovation efficiency being Shanghai, Zhejiang, Jiangsu and Anhui. Among the 27 target cities, Shanghai is characterized with the highest green innovation efficiency with an average value of 1.400 4; while Tongling and Ma’anshan are the cities with the lower efficiency, with an average green innovation efficiency of 0.429 1, 0.346 2 respectively. Among the target cities, 15 cities have a total factor productivity greater than 1 and another 12 cities have a total factor productivity less than 1. Technological progress is the main driving force for the improvement of green innovation efficiency in the Yangtze River Delta urban agglomeration, with the highest growth rate of 72.2%. In the statistical year, Zhoushan City is characterized with the fastest growth rate of factor productivity, up to 34.2%. The total factor productivity of green innovation in the Yangtze River Delta urban agglomeration is less than 1 in 2013—2015 and 2016—2017，but greater than 1 in 2015—2016 and 2017—2018, with an overall average annual growth rate of 2.7%.