Based on the theory of seepage and soil mechanics, a coupling mathematical model between the three-dimensional non-steady groundwater seepage flow and land subsidence which considers the change characteristic of porosity, permeability coefficient and water storage rate of aquifers with consolidation subsidence of aquifer was established. A three-dimensional finite element analysis method was applied to the mining of groundwater in Nantong of Jiangsu Province, based on the control requirements of land subsidence, the groundwater exploitable resources of each aquifer in all the villages was evaluated. It is shown that the total groundwater exploitable resources is 17 870.56×104 m3/a.