Beijing is a city of severe water shortage. The groundwater plays a key role in the water supply. However, the groundwater level has been gradually descending due to extensive pumping in consecutive drought years. How to satisfy the water demand and recover the groundwater level is an urgent work. With the implementation of the South to North Water Transfer Project, an opportunity has been provided for restoration of groundwater under over exploitation. On the basis of hydrogeology conditions of the Beijing plain, as well as the high-performance parallel computing platforms, a groundwater flow numerical model was established. And dynamic monitoring data of groundwater levels were used to calibrate the numerical model. The calculation results fit well with the measured data in the calibrated model. Therefore, the calibrated model can be used to predict the dynamic change of groundwater levels in the Beijing plain. The results show that several obvious depression cones of groundwater have been formed because of the rapid decline of groundwater levels in the Beijing plain in recent years. After the implementation of the South to North Water Transfer project and due to the restrictions on groundwater exploitation, the area of cone of depression will be reduced to different degrees, the central water level of depression cone will increase, and some cones of depression around wellhead will disappear. It is a benefit to relieve water shortage and control the development of land subsidence and the deterioration of the ecological environment.