The construction and operation of sluices and dams inevitably change the natural state of river hydrology and have an impact on river ecosystems. Therefore, simulating the hydrological processes of sluice-controlled rivers is of great significance to river water resource management and ecological restoration. The present study analyzed the complex characteristics of the water cycle of sluice-controlled rivers in the plains area of China including the extraction of the river network’s canal system. The treatment of sluice dams and the simulation of the base flow process of the soil and water assessment tool (SWAT) were improved. A distributed hydrological model of the sluice-controlled rivers in the plains area was constructed. Then, we applied the model to the Shaying River Basin, which has many sluices and dams. The Nash–Sutcliffe efficiency coefficient, percentage deviation, and determination coefficient were used to evaluate the model. The evaluation indices and simulation results of the three hydrological stations in the basin show that the improved SWAT model more accurately identifies the effects of the regulation and storage of the sluices and dams on runoff in the plains area and demonstrates that this model is suitable for simulating the hydrological processes of the sluice-controlled rivers in the plains area.