To study the deep foundation pit excavation of the high confined water foundation in the Yangtze River floodplain area, a Nanjing I-shaped 6 floor underground metro transfer station foundation pit excavation was selected as research object. Using finite difference software FLAC3D, numerical simulation on semi-normal and semi-reversed construction method and the cut and follow method was carried out separately, and the effects of the coupling action of the foundation pit excavation and stress seepage of precipitation on the surrounding surface settlement, lateral displacement of diaphragm wall and supporting axial force were analyzed. The findings show that: 1) in the deep foundation pit excavation project of high confined water foundation of the Yangtze River floodplain, both the surface settlement value and the continuous wall deformation value are large; 2) in the excavation of I-shaped deep foundation pit, the maximum value of surface settlement and continuous lateral displacement of wall occurs at the midpoint of the upper and lower transverse edges; 3) the surface settlement, lateral displacement of continuous wall and axial force value of transverse support in the semi-normal and semi-reversed construction method are all lower than that in the cut and follow method, conducive to controlling the lateral wall deformation of foundation pit and reducing the risk of foundation pit excavation.