Basing on the“ B-Z ”reaction model characterized by typical serf-organization，this paper analyzes the self-organization rules of enterprise system evolution with synergetic theory which is generally applied to analyze complex giant systems．The results show that studies of applying complex science methods to solve the problem of uncertain economy system are gradually progressing．but most studies remain on qualitative description or constructing simple two-dimensional variable model to simulate the phase of enterprise system evolution．By introducing“B-Z”reaction model，this paper constructs a three-dimensional variable model to describe enterprise system quantitatively，which makes the evolution rules more objective and practical，and airpries adiabatic elimination principle of synergetic theory to the problem of complex calculation caused by increased variable dimension．The combination of synergetic methods and“B-Z”reaction model is a new idea in the study of enterprise system evolution，and a favorable theoretical support for the further related study．