In the present paper, an optimization model of the ecological water replenishment quantity of Boluo Lake wetland was constructed for ecological water replenishment in the Boluo Lake National Nature Reserve based on the interval two-stage stochastic programming (ITSP) method, which scientifically allocates the ecological water resources and enhances the utilization of flood resources in order to meet the minimum ecological water replenishment quantity requirement to meet the local economic and social water demand, to restore the wetland function of the reserve, and to improve the ecological environment. In addition, it considers the ecological service value of the reserve in order to achieve a shared increase in the ecological and economic benefits. The optimization model of the ecological water replenishment of Boluo Lake wetland considered the minimum ecological water replenishment as the objective function, while the water diversion capacity, water supply capacity, water diversion sequence, functional area, and ecological service value of the Lake bubble were utilized as constraints in order to restore the ecosystem function of the Boluo Lake National Nature Reserve. The results from the model revealed that the amount of ecological water replenishment was significantly reduced after optimization simulation, with the maximum reduction range in the ecological water replenishment being −100.00% and −74.58%. In addition, the total amount of flood diversion was significantly increased, and the flood resources could be fully utilized. Moreover, the recovery effect on the lake and pond functional areas was significant and compared much better to that prior to the ecological water replenishment, which was up to 2300.00% and 1987.59%. The ecological service value also increased significantly, and the rate of this increase was as high as 23.90% and 21.58%. In the present study, an optimization model was constructed for the ecological water replenishment of the Boluo Lake wetland supplement project based on the interval two-stage stochastic programming method, which would achieve the entire scope of ecological and economic benefits of the ecological water replenishment project by realizing the ecological system reconstruction and providing a feasible and reliable plan to the decision-makers.