In lowland alluvial river systems consisting of mainstream, distributaries, and floodplain lakes, the flow dynamics are characterized by changing backwater effects and seasonal water storage and release, and the bed morphology is unstable due to frequent sediment deposition and erosion. Hence, models that can accurately and efficiently simulate hydraulic interactions with low topographic data demands are required for such water systems. In this study, we present a coupled flow routing model for the Yangtze River-Dongting Lake system by coupling a 1D hydrodynamic model for the mainstream with hydrological models for distributaries and the lake. A new approach is proposed to generate a set of rating curves to represent the combined impacts of the inflow and outlet stage on the lake storage volume, thereby an innovative hydrological routing method fully considering backwater effects is established. Additionally, an implicit fully coupled algorithm is presented to integrate the hydrodynamic and hydrological models, which demonstrates ideal numerical stability and high computational efficiency. The coupled model is applied to flow routing in the Yangtze-Dongting system, with the Nash-Sutcliffe efficiency coefficients above 0.960, and most of the mean absolute error below 0.4 m (1000 m3/s) for stage (discharge). The model is also used to evaluate the impact of topographic changes during 1998–2016 on the flow process. The results indicate that the mainstream stage has decreased notably, while the reduction of the storage capacity of the lake is not yet remarkable. For the model proposed in this paper, only hydrological data and mainstream topographic data are necessary during model development, calibration, and application. In the context of continuous channel/lake bed adjustment in the middle reach of the Yangtze River Basin, the coupled model provides an effective tool for quantitatively evaluating the hydrological regime and flood process of a river system at a full scale.