In deepening Chinese industrialization, industrial agglomeration is an important way to realize industrial transformation and upgrading, and it is worthwhile to find the sources of agglomeration effects. Starting from three features of industrial agglomeration, this paper reconstructs industrial agglomeration indexes based on geographical absolute concentration, specialized division and economic connections among industries, calculates labor and capital agglomerations in 13 manufacturing industries of China from 2004 to 2013, and finds that labor agglomeration declines slowly while capital agglomeration increases year by year. Furthermore, this paper divides the manufacturing industries into three types, namely, the laborintensive, the capital-intensive and the technology-intensive, according to common factor intensity, and carries out an empirical test of the relationship between factor agglomeration and productivity. As the results show, capital agglomeration has a significant impact on both the single and the total factor productivity (TFP) of all three industries; on the contrary, labor agglomeration only has impacts on the labor-intensive industry, a weak impact on the technology- intensive industry, and no impact on the capitalintensive industry. Therefore, the agglomeration effects of Chinese industries mostly come from the capital factor. We should pay more attention to the positive role of capital agglomeration and avoid crowding effect resulted from excessive concentration during the industrial intensive development process. Keywords: Industrial Agglomeration, Agglomeration Index, Single Factor Productivity, Total Factor Productivity, Agglomeration Effect.