This paper, by using technology of structural equation model (SEM) of the PLS model, discussed the relationship between FDI and promoting green innovation capability of MGIS. The research finds that it has a positive effect on FDI inflows to green innovation resources of MGIS inputs, but FDI information inflows have an inhibitory effect on the manufacturing green innovation human resources. At the same time, green innovation resources of MGIS inputs also have a positive effect on the green innovation capability, but the green innovation resources has an inhibitory effect on the green R&D capability. This paper also finds that based on the intermediary role of innovation resources, FDI inflows have a significant positive influence on green R&D capability and green manufacturing capability, but they have inhibitory effect on the market development capability for green products.