In this work, an interval-parameter two-stage stochastic programming (IPTSP) model of water resources allocation was established for maximizing the restored habitat area of large, rare, and endangered water birds by adjusting the recommended scheme of water replenishment under different scenarios and constraints. The established model can efficiently deal with the uncertainties, such as the interval parameters and random variables, in the management system of water resources simultaneously. A case study was conducted in the Momoge National Nature Reserve (MNNR) in northeast China to maximize the restored habitat area of large, rare and endangered water birds based on limited water resources. According to the previous studies, a water area with a depth of 0–40 cm is a suitable habitat area in the MNNR for the Siberian crane, oriental stork, and red-crowned crane. The results of the present work show that the habitat area restored by water replenishment schemes under low, medium, and high flood flow scenarios after optimization increased in comparison to 13.36 × 103 ha of the recommended scheme, with an increase of [0.62, 5.23], [1.49, 6.42], and [2.43, 7.17] × 103 ha, respectively (the two numbers within each bracket represent the lower and upper bounds of the restored habitat areas). As a result, the carrying capacity of suitable habitat areas increased by [0.82, 6.88], [1.96, 8.45], and [3.21, 9.43] × 103 birds, correspondingly. The restored wetland area of the project recommendation scheme was 34.23 × 103 ha, and that of the optimal water replenishment schemes was [29.35, 41.01], [31.02, 44.13], and [33.88, 46.04] × 103 ha, respectively under the three flood flow scenarios. The results reveal that the model constructed in this work realizes the optimization and adjustment of the initial scheme to an increased restored wetland and habitat area with an increase in the flow level. Here, the upper bound of the interval value mentioned above is significantly higher than the lower bound value, which indicates that a feasible decision space was provided for decision makers to optimize and adjust the recommended scheme on the basis of the actual situation. The model-optimized schemes significantly improved the utilization of limited water resources. The results of this study can provide valuable theoretical support for the restoration and protection of rare and endangered water bird habitats and planning and management of water resources.