Different nations construct the National Innovation System (NIS) to promote the innovation capability in the 20 century, while the results differ. To explain this phenomenon, this paper proposes the concept and taxonomy of linkage policy to analyse the policies published by the Ministry of Science and Technology (MOST) from 2001 to 2015 using the method of policy content analysis. This paper gets the conclusion that, firstly, the linkage policy could solve the problem of NIS operation failure. Secondly, China NIS had used the linkage policy with feature of ‘linear model’. Finally, this paper makes policy recommendations.