The Taihu Basin is located at the estuary of the Yangtze River, belonging to the intersection of China coastal economic belt and the inland economic belt along the Yangtze River. It is one of China's highly urbanized areas. Under the influence of continental polar air masses, maritime tropical air masses and tropical cyclones, the types of precipitation in the Taihu Basin are divided into plum rain and typhoon rain. Different weather systems lead to the different heterogeneous precipitation, which brings great challenges to flood management in the basin. Taking the spatial and temporal differences of flood risk caused by different weather systems into consideration, this paper analyzed the flood risk based on Copula theory. In terms of time, the probability distribution of the precipitation dominant factors was used to divide the flood period into the plum rain period and the typhoon period. In terms of space, we clustered the study areas in the plum rain period and the typhoon period respectively by the Archimedean copula function. Finally, the flood disaster risk during the plum rain period and the typhoon period was analyzed. The results indicate that the flood period of the Taihu Basin is divided into the plum rain period (June 24 to July 21) and the typhoon period (July 22 to September 22). According to the joint distribution of sub-region precipitation and the Taihu Lake water level, the Taihu Basin is divided into three sub-regions (P-Ⅰ sub-region, P-Ⅱ sub-region and P-Ⅲ sub-region) in the plum rain period, while the Taihu Basin as a whole for flood risk analysis in the typhoon period. In the future, the probability of the drainage adverse in the Taihu Basin during the plum rain periods and the typhoon period is 2.4% and 1.1%, respectively. It is of great significance for the Taihu Basin to adjust the schemes of design storm and utilize flood resource and make the decision of real-time scheduling for flood control and drainage.