The inputting decision process of research and development collaboration between the core enterprise and the agent in the knowledge chain is analyzed. In the collaboration process, the agent takes the responsibility of research in the basic stage and the core enterprise undertakes the innovation in the application and development stage. The research indicates that the higher the research stage benefits the core enterprise gains, the higher the elastic coefficient of input-output at the research stage is, the core enterprise gives more subsidies to the agent under sequential game. Both the core enterprise and the agent are willing to invest more under cooperative game than that under sequential game. Moreover, the distribution coefficient of cooperative rent from incremental innovation income produced by cooperative game is negatively correlated to the risk aversion degree, and it has nothing to do with the bargaining ability, meanwhile, the premium subsidy has a positive correlation to the risk aversion degree and the bargaining ability.