A method of standard syntaxis of the flood control and drainage based on the theory of water level safety margin is constructed, and the northern part of the Taihu Lake Basin is used as the study area to analyze the cohesion between the sub-basin flood and urban drainage standards. Through the trial calculation of different simulation schemes, the effect of changes of sub-basin flood and urban drainage standards on the inflow and outflow volume in key sections is analyzed, and the design combination of sub-basin flood and urban drainage standards is proposed based on the evaluation method of water level safety margin. The results indicate that the current sub-basin flood and urban drainage standards of the northern part of the Taihu Lake Basin basically can resist the flood with a return period of 50-year. However, the capacity and demand of flood control and drainage at the sub-basin and urban are incohesion, which shows that the water level in the urban is far lower than the flood control design water level, while the sub-basin water level is close to or even higher than the flood control design water level and even slightly higher than its flood control capacity. There are significant differences in the characteristics of changes in the flood discharge pattern caused by the improvement of flood control standards in different sub-basins. The flood control capacity of Wuchengxiyu District and Yangchengdianmao District is improved by expanding the flood discharge to the Yangtze River, while the Huxi District is profited by expanding flood discharge to the Taihu. Limiting the discharge volume of polder of urban has limited effect on alleviating the flood control pressure in the external area of urban. Finally, the sub-basin flood standard with a return period of 50-year and the urban drainage standard with a return period of 20-year in the north of Taihu Lake Basin are the design combination of standard syntaxis.