Under the background of the transformation from "local space" to "mobile space", innovation is gradually transformed from the innovation of a single innovation subject to the collaborative innovation of many innovation subjects. This paper analyzes the effect of collaborative innovation on urban innovation efficiency by combining the panel data of 41 prefecture level cities in Yangtze River Delta city cluster. The empirical results show that :(1)The level of collaborative innovation has a significant effect on the efficiency of urban innovation; (2)The level of collaborative innovation has regional heterogeneity on urban innovation efficiency. In the collaborative innovation, the level of urban collaborative innovation in the sub core region has the greatest effect on innovation efficiency, the core region is the second, and the role of the collaborative innovation level of the marginal cities on innovation efficiency has not been significantly reflected.