Abstract: Green innovation is the key to cultivating new drivers of urban development. This paper is devoted to analyzing and comparing the green innovation efficiency and spatial association characteristics of 26 cities at or above the prefectural level in the Yangtze River Delta Urban Agglomeration(YRDUA). It is of vital importance to promote higher quality integrated development of the YRDUA. Considering that the traditional DEA model does not consider "relaxation" of factors and cannot reasonably solve the efficiency evaluation problem under the condition of non-expected output, this paper uses Super-SBM and GML index as new models to measure the green innovation efficiency at urban scale, and depicts the spatial characteristics of the YRDUA. The result shows that:(1) The green innovation efficiency of 26 cities in the YRDUA is on the rise as a whole, and the driving forces are mainly from technical efficiency, while technological progress lags behind technological efficiency. (2) From the perspective of spatial correlation, the difference of green innovation efficiency between 26 cities tends to narrow in the YRDUA, and the green innovation efficiency of the YRDUA tends to be integration. (3) There exist four types of combinations between the efficiency of urban green innovation and the level of economic development in the YRDUA, i.e., high-high, high-low, low-high and low-low. Finally, some policy suggestions are put forward. High-high cities should further improve green innovative technologies and gradually abandon or upgrade industries with high pollution and high input; then low-high cities are more suitable for capital-intensive development; high-low cities should realize the coordinated development of green economy by improving the conversion efficiency; low-low cities should pay attention to the problems of industrial structure and speed up the improvement of the efficiency of scientific and technological research and development.