This paper first portrays the equilibrium payoff of enterprise's cooperation of environmental governance based on the Cournot model. Secondly, the evolutionary game model in complex networks is adopted to depict the evolution of environmental governance cooperative behavior among enterprises. Further, the evolutionary process of environmental governance cooperative behavior of enterprises is simulated considering the supervision behavior of government and the reputation evaluation behavior of environmental social organization. The results show that the cooperation level of enterprise group under self-organization condition will reach a low level; the supervision of government can enhance the cooperation level of enterprise group with high betrayal tempatation while it has limited effect on enterprise group with low betrayal tempatation. The reputation evaluation behavior of environmental social organization can realize reputation effect to improve the the cooperation level of enterprise group with high betrayal tempatation. The enhance of reputation sensitivity can optimize equilibrium distribution of reputation and it can strengthen the reputation effect on cooperation level. Based on the analysis above, the suggestions to effectively improve cooperation level are given.