Abstract: With the gradual advancement of the development strategy of the Yangtze River Economic Belt and the continuous improvement of the urbanization level, the drainage capacity of the middle and lower reaches of the Yangtze River is increasing. When the drainage of waterlogging areas along the river encounters the main stream flood of the Yangtze River, the flood pressure of the main stream will deteriorate while the waterlogging in the waterlogged area will be worse. Based on the investigation and analysis of the drainage capacity of the waterlogging areas along the middle and lower reach of Yangtze River, we designed two drainage situations, the drainage from various reaches and the drainage from various drainage zones(urban drainage and agricultural drainage), and analyzed the impact of the two drainage cases on the flood level of the main stream in typical years by using integrated hydrological model. The results showed that the contradiction between flood defense of mainstream and waterlogging mitigation will only be serious in huge flood year, and the drainage quantity had a relatively small proportion, so its effect mainly manifested on raising water level.