For the upstream and downstream water pollution conflict, a third-party mediation model is established based on the inverse problem of graph model for conflict resolution. The model is used to obtain an equilibrium that minimizes the preference adjustments on the premise of fully considering the bottom line of preferences of both parties of the conflict. Based on the inverse problem theory, a 0-1 multi-objective programming third-party mediation model is proposed, and the model solution is designed. Finally, the model is applied to the water pollution conflict in the upstream and downstream areas, which further verifies the effectiveness of the model in solving mediation schemes and adjusting preferences. The third party can resolve the conflicts by using the model. The optimal state can be achieved that can make the upstream and downstream areas make the minimum preference concession so as to provide reference for the mediation of conflicts for water resources.