The Quaternary loose layer of Yangtze floodplain area is a huge thick and complex aquifer with rich groundwater, which has great influence on deep foundation pit engineering. This paper analyzes the characteristics of dewatering project for the foundation pit in Nanjing Meizizhou river-crossing tunnel project, dewatering designs were made for each segments, and proper dewatering well structure was selected based on the features of different segment, the aquifer above the excavation surface was dredged by whole hole filling filter material with good dewatering effect. Standby wells were prepared in the segments where there was big water level difference between inside and outside pit to prevent piping caused by the defect of enclosure, increase security for foundation pit and effectively protect the surrounding environment.