Regional economic integration is an endogenous need for China's development. The Yangtze River Delta city clusters are highly concentrated in regional resources and are an excellent growth soil for technological innovation. They are also an important gateway for the country to participate in world economic exchanges. Therefore, studing the innovation efficiency of city cluster is of great significance. Based on the CCR-DEA model, this paper measures the innovation efficiency of the Yangtze River Delta urban agglomeration, and uses the SDM model to study its influencing factors in terms of regional economic development level, Internet penetration, and government support. The result is that (1) The innovation efficiency of the triangle city group is relatively high and it exhibits HH agglomeration spatial characteristics (2) The level of regional economic development will significantly promote the improvement of innovation efficiency, and government support will hinder the improvement of innovation efficiency.