Abstract: Affected by the changing environment including forth-to-third-class channel upgrading project, underlying surface condition and extreme climat, the Southern Jiangsu Canal has become a prominent weak link in the flood control systems of Taihu Lake Basin with the characteristics of "fast rising water, slow retreating water, higher water level". Based on the measured hydrological data and combined with the hydrodynamic model, this work simulated the actual flooding process of the southern Jiangsu Canal during the major flood in 2016. The results show that after the implementation of various treatment measures, the flood drainage of the canal can be solved in stages and the flood level along the canal can be reduced. The study found that in the Huxi hydraulic section of the southern Jiangsu Canal, the concentration of channel is dominated by drains northward into the Yangtze River and discharge along the southern Jiangsu Canal, where the water goes in the Wucheng Xiyu hydraulic section and the Yangcheng Dianmao hydraulic section would be affected by the flood (tide) water level on both sides of the Yangtze River and Taihu Lake. When the water level of the external Yangtze River is high, the storage and slow drainage through the canal is the main flood outlet. Combined with the actual situation of the region, this work put forward countermeasures according to the governance philosophy of "expanding external discharge, increasing storage capacity, and controlling downward release".