With the background of innovation cooperative behavior in the innovation network under the guidance of the core enterprise, and the heterogeneity of the initial public goods game as the benchmark, through introducing various mechanisms, this paper enhances the effect and significance of the level of cooperation between network members, and selects the optimal mechanism. The results show that the effect of incentive mechanism and leadership mechanism alone can not maintain the high level of enterprise cooperation; the joint mechanism of punishment, rewards and punishments and leadership mechanism can effectively mitigate the vulnerability of enterprise cooperation.