Large enterprises are the complex, nonlinear and dynamic system in nature. The traditional analytical methods can not include the nonlinear characteristics of the systems and operation into the dynamic evolution of the analytical framework for the enterprises. And the System Dynamics(SD) emphasizes an the decisive role between the system structure and the system behavior and explains the relationship throughthe interaction of various elements of the dynamic behavior in the system. Therefore, the SD is used to establish an analysis model of original innovation systems and makes a research on the various flowing factors in order to analysis in the dynamic evolution process of innovation in the large-scale enterprises. Finally, the factors that impact the original innovation output of large enterprises are given and the policy guidance for the high-performance development in the original innovation system of the enterprise is provided.