At present，with the frequent occurrence of transboundary water pollution incidents，many social problems have been caused. Although relevant local governments and competent departments have successively issued relevant policies and regulations to control transboundary water pollution，the results are not very satisfactory. Therefore，how to strengthen the treatment of transboundary water pollution? How to set unified standards on trans-regional water pollution control? This has also become the focus of the relevant functional departments. In the process of the actual cross-regional cooperation in water pollution control，the decision-making environment of negotiating budget costs is complex and changeable，which makes it difficult for decision-making experts to use specific values to express the accurate judgment of decision-making information. Based on the background of collaborative water management and the minimum cost consensus model in group decision theory，this paper constructs a scenario robustness minimum negotiation cost model for the purpose of completing water pollution control negotiations with the minimum budget. In view of the fact that scenario robust thinking can effectively reduce the uncertainty in cross-domain cooperative governance of water pollution according to actual needs，it helps decision makers to make more robust and effective decisions in complex and uncertain decision environments. Numerical experiments show that the model can make effective budget plans according to the actual situation，and jointly solve the budget formulation problem in the cross-regional cooperative governance of water pollution by carrying out the joint prevention and control of the surrounding boundary water pollution environment.