Through selecting the panel data of 27 manufacturing industries in our country from 2009 to 2013, this paper makes an empirical test on the impact of FDI on the independent innovation capability of Chinese domestic-funded manufacturing industries from the perspectives of innovation input and innovation output. The findings of this study show that: FDI promotes the innovation input of Chinese domestic-funded manufacturing industries, but not obviously; FDI plays a significantly positive role in promoting the innovation output of Chinese domestic-funded manufacturing industries. This proves that although FDI has a significant effect on promoting the independent innovation capability of Chinese domestic-funded manufacturing industries, the positive effect is limited. In addition, the scale of enterprises and the degree of market competition have significantly promoted the increase of independent innovation investment in China’s manufacturing industry, and the investment of R&D staff and R&D funds have significantly positive effects on the independent innovation output of Chinese domestic-funded manufacturing enterprises.