Objectives: In recent years, along with the increasing of underground engineering constructions, which presents deep excavation pit, largescale, complex shape and other characteristics. The geological environment is very complicated in the lower reaches of the Yangtze River, as a result, the supporting structure design and construction is very difficult. Taking a large underground transportation hub project along the Yangtze River in Nanjing as an example, the paper discusses the important role of the research of geological environment on the design of the supporting structure of deep foundation pit. The structure of the project has three layers. The bottom layer would connect riverbottom tunnel, and the upper two layers would connect nearby venues and a plurality of ground road. The foundation pit excavation is very deep, the excavation depths are very different and the shape of foundation pit is very irregular. The project is located on the west side of Nanjing Youth Olympic Center, the place that is near the Yangtze River embankment. The Quaternary loose sediments are widely distributed in this area. Methods: This paper aims at the core area of the super large foundation pit engineering, analyzes its engineering geological conditions and raises the possible engineering geological problems. According to the function and shape of the foundation pit, the soil layer of the foundation pit is partitioned and layered from the plane and section and the supporting structure design has been optimized. The scheme of foundation pits supporting was a combination method of open cut excavation in the upper part and the diaphragm wall in the lower part. The successful completing and deformation monitoring of foundation pit has illustrated the rationality of the design scheme. Results: It solves the problem of large irregular foundation pit construction technology, improves the construction speed and reduces the construction cost. Conclusions: This result can be applied for the design of support scheme and deformation control of some super large foundation pit engineering in the area of the Yangtze River.