Pollutant discharge permit trading is an effective economic means to realize equilibrium development between pollutant treatment and water quality improvement. On the basis of summarizing the study characteristics of pollutant discharge permit trading at home and abroad, we present the study framework making treatment cost minimizing and the risk of low water quality minimizing as objective functions. Combining the application scope of the Non-dominated Sorting Genetic Algorithm-Ⅱ(NSGA-Ⅱ), Young Bargaining Theory (YBT)and Initial Discharge Permit Allocation model (IDPA), we construct Discharge Permit Trading model (DPT) considering the related factors of watershed pollutant treatment. By virtue of nonzero-sum game and theoretical framework of trading model, we describe the calculation process of optimization model. We choose typical watershed as a realistic example to test the efficiency and applicability of methodology for developing pollutant discharge permit trading. Finally, we give the perfection suggestion and application prospect forecastin.