Based on the datasets drawn from annual surveys of Chinese manufacturing firms,and the Nicholas Bloom’s model,this paper analyzes the influence of the R&D intensity on firm productivity. The results show that R&D does have a significant positive effect on firm productivity. In consideration of the spatial economic differences in China,further analysis found that the effects of R&D on firm productivity are stronger in cities with relatively more Marshall intensive agglomerations and are weaker in cities with relatively more intensive Jacobs or Krugman agglomerations. Therefore,“free riding” in R&D exists in cities with relatively more intensive Jacobs or Krugman agglomeration. Finally this paper demonstrates the different effects of agglomerations on R&D in view of firm size and ownership structure respectively.