Excessive groundwater withdrawal has caused severe land subsidence worldwide. The pore water pressure and the deformation of pumped hydrostratigraphic units are complex. A fully coupled three-dimensional numerical simulation was carried out for different pumping plans in this paper. When groundwater is pumped from a confined aquifer, the great compaction occurs in the pumped aquifer and its upper and lower adjacent aquitard units. Land subsidence is smaller and the area affected by land subsidence is greater when groundwater is pumped from the deeper confined aquifer. The pore water pressure in the pumped confined aquifer changes immediately with pumpage. In the adjacent aquitard units, however, the pore water pressure increases in the early pumping time and decreases in the early recharging time. The decrease in the pore water pressure vertically spreads from the interface between aquitard and pumped aquifer to the other surface of the aquitard. The pumped aquifer compacts and rebounds immediately with pumping and non-pumping or recharging actions, while the compaction and rebounding of the aquitard units clearly lag behind. The compaction of the adjacent aquitard unit first occurs near the interface between aquitard and pumped aquifer units, and the compaction zone spreads outward as the pumping goes on. The aquitards may expand vertically within some zones. Due to the inelastic deformation of soil skeleton, different pumping plans result in different land subsidence. For the same net pumpage, maximal land subsidence and horizontal displacement are the smallest for constant discharge and the greatest for recharge-discharge cycle.