Through analyzing enterprise system operation rules based on synergetics theory, this paper aims to decide the strategic input of enterprise system. In synergetics, enterprise system's threshold reveal the relationship between external control variables and state variables of enterprise systems, which could be reached by changing control variables. And then, the enterprise system would be able to achieve the self-organization evolution under the servitude of order parameter. When determining the strategic input scale of enterprise system, the order parameter should be taken as the strategy center. As the enterprise system control variables, human, finance and technology are also the objects for deciding the enterprise input scale, thus, we can determine the direction and scale of enterprise system input. The application of synergetics theory has developed a new path to decide the strategic input of enterprise system.