Based on data of 285 cities in China from 2003 to 2012, this paper explores the relationship between industrial agglomeration and total factor productivity by using an econometric analysis method. The theoretical analysis show that the mechanisms of industrial agglomeration promote total factor productivity are that knowledge or technology spillover and technological innovation diffusion. Empirical analysis shows : (1)Manufacturing agglomeration and producer service industrial agglomeration both can help to promote total factor productivity, but the impact of producer service industrial agglomeration on total factor productivity is greater. And manufacturing agglomeration mainly through technological progress to promote total factor productivity, while producer service industrial agglomeration mainly through technical efficiency to promote total factor productivity;(2)Region-specific analysis reveals that the impact of industrial agglomeration on total factor productivity of inter-regional are different;(3)The positive impacts of Manufacturing agglomeration and producer service industrial agglomeration on the total factor productivity and technical efficiency mainly by the pathways of human capital and infrastructure, while the promotion on technological progress mainly by the pathways of human capital, FDI and infrastructure. Moreover, in all these pathways, infrastructure makes a significant contribution.