Abstract: It is very important to scientifically evaluate the management benefits of flood diversion systems of medium and smallsized rivers. Based on the principle of water balance, this paper puts forward the benefit evaluation method of flood diversion river systems control measures, and takes Niutun River in Chaohu Basin as an example to analyze the changes of effective external drainage through Niutun River in Chaohu Basin before and after the implementation of the Niutun River system control project during the Meiyu period in 2020. Combined with the actual economic and social conditions of the basin, the flood defense and disaster reduction benefits of the project are estimated. The results show that after the implementation of the Niutun River system control project, the broken area above Chaohu Gate and in Yuxi River Basins can be reduced to 2 687 hm² and 1 473 hm² respectively, and the loss of flood disaster can be reduced to about 657 million yuan. The study shows that the control measures of flood diversion system of small and medium-sized rivers based on increasing the safety discharge and improving the flood control standard of embankments can effectively reduce flood losses, form good flood diversion benefits, and provide a new idea for the study of the control measures of flood diversion river system.