Abstract: Based on the relevant data from 1990 to 2010 of Fujian Province, this paper analyzed the relationship between export commodity structure and FDI in Fujian by using the methods of Stationary Test, Cointegrated Test and Granger Test.The results showed that they had the longrun equilibrium relationship, and FDI could optimize the structure of export commodities greatly.Last, this paper put forward the solutions, which include optimizing FDI environment, guiding foreign investment to hightech industries, and increasing the use of foreign investment to develop the leading industries.