Based on the geological and hydrogeological conditions, and in situ hydrogeological tests of the emergency groundwater source in Nantong City, China, a 3D numerical model of the heterogeneous anisotropy in the study area was established and calibrated using data from pumping and recovery tests. The calibrated model was used to simulate and predict the water level of the depression cone during the emergency pumping and water level recovery. The results showed that after seven days of pumping, the water level in the center of the depression cone ranged from −51 m to −55 m, and compared with the initial water level, the water level dropped by 29 m to 32 m. The calculated water level has a small deviation compared with that of the analytical solution, which indicates the reliability and rationality of the numerical solution. Furthermore, during water level recovery, the water level of pumping wells and its surroundings rose rapidly, which was a difference of about 0.28 m from the initial water level after 30 days, indicating that the groundwater level had recovered to the state before pumping. Due to the emergency pumping time is not long, the water levels of Tonglu Canal, surrounding residential wells, and other aquifers will not be affected. After stopping pumping, the water level recovers quickly, so the change of water level in a short time will not lead to large land subsidence and has little impact on the surrounding environment.