Based on the shallow and deep soil deformation data, the deformation data of the aquifer and the water level, the deformation data of the infrastructure (mainly the subway tunnel, the elevated and the ground roads), we studied the deformation characteristics of the deep soil layer and shallow soil layer in Shanghai, and discussed the deformation characteristics of subway tunnels, elevated and ground roads under the combined deformation of shallow and deep soil layers, and reached the following conclusions. First, the shallow soil layers are in continuous compression, and the total amount of compression is small. The deep soil greatly compressed before 2009, and has gradually expanded since then. Second, the deformation of the confined aquifer in Shanghai is closely related to the water level of the soil layer. When the water levels of the first, second, third and fifth aquifer rise, the soil layer rapidly expands. The expansion of the fourth confined aquifer is lagging behind the rise of the soil water level. Last, deep soil layers have similar deformation trend with the infrastructure, and shallow soil layers with different thickness affect the deformation of the infrastructure. The infrastructure near the deep soil layer has obvious uplift deformation, accompanied by the expansion of deep soil layer. Under the same conditions, the infrastructure with thick shallow soil layer shows greater settlement than that with thin shallow soil.