This paper first calculated the total factor productivity(TFP) growth of 27 manufacturing industries in Chongqing from 2000 to 2011 using the DEA-Malmquist method, then empirically tested the effect of industrial agglomeration on the TFP growth of manufacturing industries in Chongqing, also examined the moderating effect of R&D input, foreign direct investment(FDI) and industry property in this relationship. The result reveals that Chongqing manufacturing industry has an average annual growth rate of 16.7% from 2000 to 2011. The result indicates that industrial agglomeration positively influences on the TFP growth of manufacturing industries in Chongqing. The result also reveals that R&D input positively moderates the relationship between industrial agglomeration and the TFP growth, and FDI negatively moderates the relationship between industrial agglomeration and the TFP growth. In addition, the result shows that industrial agglomeration has a positive effect on the TFP growth in capital- and technology-intensive industries, but has no significant effect on the TFP growth in resource- and labor-intensive industries.