Abstract: Based on the statistic data from 2000 to 2006, effects of the regional innovation system on the capital input and innovation input from FDI, and the spillover effects of FDI on the productivity and innovation performance of local enterprises are in vestigated. It is found that the regional economic circumstance,regional innovation capacity have positive effect on FDI input and innovation input. The productivity spillover effect of FDI from west countries are negative comparing with the FDI from Hong Kong, Macau, and Taiwan area in the short term, whereas MNCs from west countries which are comparably more advanced in technology level can improve the technology level of local firms and cause spillover effects in the long terms.