This paper conducted systematic research on the mute feed effect caused by the change of project scheduling conditions of flood and waterlogging between three levels of basin, sub-basin and urban in the Taihu Basin. Taking the Taihu Basin and its internal water conservancy districts and towns as an example, different simulation conditions and scheduling scenarios were designed based on the idea of control variables, and the flood movement process in the basin under different flood control project conditions and scheduling schemes at various levels was quantitatively simulated. The mute feed effect of flood and waterlogging was analyzed from the aspect of water level variation at various levels. The results indicate that properly raising the drainage control water level of urban flood protection and waterlogging drainage project can relieve the flood control pressure of basin and sub-basin while ensuring the safety of urban internal flood control and drainage, but with limited effect. Modestly reducing the control water level of sub-basin drainage project along the Yangtze River and Hangzhou Bay can significantly reduce the water level of the Taihu Lake and sub-basins, and can also have a certain effect on the internal water level drop of urban. The capacity of flood discharge of the basin has highly increased with implementation of the flood releasing projects such as the Wusong River, and can also substantially reduce the water level of the Taihu Lake and sub-basins. However, further implementation of the sub-basin flood protection and waterlogging drainage project could only lower the internal water level of sub-basins, with almost no impact on the basin and the urban.