The mean head gradient plane of the irregular triangle column volume was proposed to solve the simplified numerical simulation problem of groundwater in irregular and declining aquifer-aquitard system. According to the results of water balance in a finite volume based on the mean head gradient plane, the net lateral flux and elastic storage of the element were calculated. The vertical water flow flux between upper and lower layers was computed by the finite difference method. The simplified 3D numerical model was obtained from the proposed method and applied to simulate the groundwater flow in different hypothetic groundwater exploitation conditions. The comparison of the results of the proposed model with Visual Modflow and Feflow showed good agreement of the three models and its advantage over Visual Modflow for the declining and irregular aquifer-aquitard system.