Abstract: Water inrush and flooding wells are common disasters in karst fissured aquifer water filled mine with complex hydrogeological conditions, which have the characteristics of causing large losses and difficult governance and recovery. In Southwest China, there are a large number of lead-zinc and bauxite mines affected by water filling of Upper Paleozoic Carboniferous and Permian karst fissure aquifers, and there are potential hazards of water inrush and flooding wells. but there are few literatures in the past. Taking Maoping Lead-Zinc Mine of Yiliang as an example, by studying the water level of the observation hole after water inrush, the change of the water intake point of the original roadway, the seepage field of groundwater and the structure of water diversion after water inrush are studied, the source of water inrush and the water diversion channel are further verified, and the disaster mechanism of water inrush is summarized. It adopts the combination governance plan of “control, blocking and sealing” is adopted. Firstly, it constructs the water blocking section in the upper roadway by directional penetrating hole construction, and then carries out the water diversion fault grouting and sealing in the water source area of the water inrush, which not only treats the symptoms but also the local root causes, so as to treat the water inrush safely and efficiently and restore the production. Avoiding the disadvantages of traditional governance plan of “drainage before plugging” in the underground and “plugging before plugging” in the surface, which may further deteriorate hydrogeological conditions, poor grouting effect, and large safety risks of downhole close plugging. The analysis and summary of research methods for water inrush sources and channels, the mechanism of disaster caused by water inrush and the combined governance plan of “control, block and seal” adopted have strong reference significance for the treatment of water inrush flooded wells in similar large water mines in Southwest China.