With the continuous urbanization and industrialization in recent years, different stakeholders in the same basin meet local water needs and compete for water resources, which hinders economic development and ecological protection of the basin. Different stakeholders conceal information about their own strategies and preferences to protect their vested interests, making it difficult for third-party regulators to develop optimal operational policies for the joint use of water resources in the basin. Therefore, the research objective of this study is to propose a new grey inverse Graph Model for Conflict Resolution (grey inverse GMCR), and apply the new method to the complex problem of water allocation and environmental governance with the Poyang Lake basin conflict. The new GMCR model proposed in this study can solve the cost minimization problem of a third-party mediator that manipulates decision makers (DMs)’ grey preferences to achieve desired outcomes. The results of the equilibrium analysis show that upstream areas' preferences mainly affect the result of water resource conflicts in the PLB, and establishing a scientific mechanism to compensate the water resources protection cost borne by the upstream areas would be a cost-effective way to realize the sustainable development of the basin as a whole.