As an important topic of spatial economics, the industrial agglomeration is studied, home and abroad, mostly from the perspective of production factors. Both theoretically and empirically, this discussion of the accumulation effect of industrial agglomeration on human capital ignores regional heterogeneity in most cases. As a matter of fact, for countries with vast territory such as China, there is significant heterogeneity among regions and the human capital accumulation effect on industrial agglomeration may vary greatly. Using the provincial panel data of China from 1997 to 2015, this paper empirically examines the effect of manufacturing agglomeration on human capital accumulation in various regions. Results show that for the total sample, manufacturing agglomeration in China significantly promotes the constant increase of regional human capital. From the perspective of regional heterogeneity, the empirical test of sub-samples of coastal regions and inland regions show that only coastal regions enjoy significant positive effect of human capital accumulation on manufacturing agglomeration while inland regions don’t. The policy implication of this conclusion is that to better exert the role of industrial agglomeration, China must explore and implement at regional level differentiated paths and strategies of regional open-up and industrial development .