Abstract: Firstly, this paper measures the level of innovation efficiency by Malmquist index. Then, based on 2003-2012 dynamic panel data, this paper test the impact of Industry Agglomeration on Innovation efficiency in all and different types of factor intensity Manufacturing industries. The conclusion is as follows: From the whole manufacturing industries perspective, industry agglomeration can effectively increase innovation efficiency; form different types of factors intensity perspective, only technology-intensive industries can effectively increase innovation efficiency, but this impact is not significant in labor-intensive and capital-intensive industries.