Based on the existing classification system of nationwide groundwater over-development area, we improve this system through subdividing the groundwater over-development area in a case study in Jiangsu Province, with consideration of the management and actual situation of the over-development area in Jiangsu Province. We present a classification management model for the groundwater over-development area and propose its application conditions: for the area with damaged geological environment due to over-development of groundwater, the development of groundwater is prohibited; for the area with a declining water level or a water level that tends to be stable but is below the early warning line, the groundwater development amount should be reduced; and for the area with a water level above the early warning line, the current status of groundwater development can be maintained.