China’s economy has entered a new normal period of speed shift, forming a new spatial carrier of regional development dominated by urban agglomerations. Standing at the forefront of innovation driven reform, the Yangtze River Delta urban agglomeration plays an important role in transforming the economic driving mode, promoting the upgrading of industrial structure and achieving highquality economic development.Based on the data of innovation activities of Yangtze River Delta urban agglomeration from 2007 to 2017, the paper analyzes the spillover characteristics of innovation efficiency by using super efficiency model and spatial econometrics. The results show that the overall spatial spillover effect of innovation efficiency in the two stages is significant, in which the efficiency in the stage of innovation restrains the transformation of economic value of surrounding cities, and the efficiency in the stage of economic transformation promotes the innovation of surrounding cities. The results also show that there is significant value chain spillover effect between the two stages of efficiency, in which the effect of economic transformation stage promoting innovation stage is 0.188, and the effect of innovation stage promoting economic transformation stage is 0.071.