With the further advance of China's market-oriented reform, the traditional economic development model is unsustainable. Adjusting the industrial structure, eliminating backward production capacity, vigorously developing hi-tech industry gradually become a consensus. Based on the panel data of 30 provinces (cities and districts) in 2000-2014, this paper firstly studies the interactive mechanism between FDI and high tech industry agglomeration. And then through the relevant theoretical analysis, it concludes that the FDI, and new economic geography factor and high tech industry agglomeration among the internal mechanism. On this basis, by constructing the location entropy index of the hi-tech industry cluster, this paper constructs the panel simultaneous equation empirical model(SEM)between the three with dividing the eastern, central and western three areas respectively empirical test. Research results show, as a whole, the FDI and high tech industry agglomeration promote each other, new economic geography factors also favor the high tech industry cluster. But there are some differences in the eastern middle and western regions.