This paper breaks the research paradigm of foreign R&D input directly affects independent innovation output, proposing the spillover path that foreign innovation input directly affects the domestic innovation input and indirect impact on domestic innovation output, constructing innovative input、innovative output two-stage model and theoretical framework of joint analysis. From the dimensions of two kinds of innovation factors capital and labor, researching on the influence of foreign enterprises innovation input on the domestic enterprises independent innovation. Based on a panel data of eleven sub- industries of China’s high-tech industry from 2004 to 2012, showing that foreign innovation input has both inhibitory effect and promoting effect on independent innovation，foreign innovation capital input will restrain the innovation output of domestic，foreign innovation labor input will promote the innovation output of domestic.