Based on analyses of the theories of groundwater unsteady flow in deep well dewatering in the deep foundation pit, Theis equations are chosen to calculate and analyze the relationship between water level drawdown of confined aquifer and dewatering duration. In order to reduce engineering cost and diminish detrimental effect on ambient surrounding, optimization design target function based on the control of confined water drawdown and four restriction requisitions based on the control of safe water level, resistance to throwing up from the bottom of foundation pit, avoiding excessively great subsidence and unequal surface subsidence are proposed. A deep well dewatering project in the deep foundation pit is optimally designed. The calculated results including confined water level drawdown and surface subsidence are in close agreement with the measured results, and the optimization design can effectively control both surface subsidence outside foundation pit and unequal subsidence as a result of dewatering.