When there is reservoir control in the upstream of the watershed, the storage coefficient K and weighting coefficient X of the Muskingum method are difficult to calibrate through measured data. To estimating K and X , a relationship between the K and X and physical characteristics of the river channel is established. Then, the Muskingum method is used to derive the inter-basin flood by routing the upstream inflow to the downstream, and subtracting the upstream routed flood from the downstream flood to obtain the inter-basin flood. The example of inter-basin flood calculation from Qingfengling Reservoir, Xiaoshiyang Reservoir to Juxian in the Shuhe River Basin shows that the difference between the inter-basin flood calculation method based on the Muskingum method and the Xin’anjiang model is minor, but the former method can consider the differences in hydraulic characteristics of different river sections for parameter estimation.