Reservoirs alter the flood propagation process. Considering that many reservoirs have different flood limit water levels and flood control storage capacities during different flood seasons, we propose a modified reservoir index. In this study, we construct four types of non-stationary statistical models, taking time t, antecedent rainfall P, and the modified Reservoir Index MRI as candidate explanatory variables. Then we compare the simulation effects of different models. The equivalent reliability method and the extreme value distribution method considering the flood staging are proposed to calculate the flood design values at different return periods for downstream sites of the reservoir. The calculation results at the Huangzhuang Hydrological Station in the lower Hanjiang River in China show that the flood occurrence time in the upper Hanjiang River and its corresponding reservoir seasonal flood limit level and flood control storage capacity directly affect the flood in the downstream river. The non-stationary model incorporating P and MRI as explanatory variables achieves the best fit for the flood. Compared with the existing reservoir indices, MRI can better describe the impact of the upstream reservoir group on the flood sequence. The calculation results of the equivalent reliability method and the extreme value distribution method are comparable. The impact of the staged setting of flood limit water levels should be fully considered. The results of the equal reliability method and the extreme value distribution method can provide a reference for the design of flood control projects.