The Quaternary loose soil of the Yangtze floodplain area is a thick and complex aquifer with typical binary characteristics of geological structure, containing thin interlayer, leading to the vertical permeability far less than the horizontal direction, which has great influence on the dewatering of deep foundation pit engineering. In the river channel, underground traffic system of Qing’ao axis and the related works of Meizizhou in Nanjing, by the full use of the advantages of diversion infiltration technology, it is successful to dewatering the upper formation of the basement to achieve a safe and dry work environment, meet the requirements of foundation pit excavation and save a great deal cost of the project, which has very good reference for deep foundation pit engineering with similar hydrogeological conditions.