Medical waste ,belonging to one of top-ronking toxic wastes, should be safely deposed of. The characteristics and harmness of the medical wastes are introduced, and the practical status of medical wastes in Chongqing three gorges region, including waste management and disposal methods, is investigated. Because of the special characteristics of the waste, the paper proposes some measures for managing and separate collection and treatment in the region, including separate collection, sealed transportation, pretreatment, incineration and safe landfill, so that the ecological environment and water resource can be protected from pollution in the Three Gorges region.