The Momoge National Nature Reserve (MNNR) is located at the intersection of Nenjiang and Taoer Rivers in Baicheng City, Jilin Province, where the Taoer River is the main source of water for the nature reserve. However, due to the construction of the water control project in the upper reaches of the Taoer River, the MNNR has been in a state of water shortage for a long time. To guarantee the wetland function of the nature reserve, the government planned to carry out normal and flood water supply from Nenjiang River through the West Water Supply Project of Jilin Province. Therefore, how to improve the utilization of flood resources effectively has become one of the key issues of ecological compensation for the MNNR. In this paper, a flood resources optimal allocation model that is based on the interval two-stage stochastic programming method was constructed, and the corresponding flood resource availability in different flow scenarios of Nenjiang River were included in the total water resources to improve their utilization. The results showed that the proportion of flood resources that were used in the MNNR after optimization was more than 70% under different flow scenarios, among which the proportion of flood resources under a low-flow scenario reached 77%, which was 23% higher than the proposed increase. In addition, the ecological benefits of low, medium, and high flow levels reached the range of 26.30 (106 CNY) to 32.14(106 CNY), 28.21(106 CNY) to 34.49(106 CNY) and 29.41(106 CNY) to 35.94(106 CNY), respectively. According to the results, flood resources significantly reduce the utilization of normal water resources, which can be an effective supplement to the ecological compensation of nature reserves and provide a basis for the distribution of transit flood resources in other regions.