Taking a foundation pit near the urban rail transit structure in southern Jiangsu as an example, the soil parameters were obtained by inverse analysis and three-dimensional finite element method simulations. On this basis, the influence of different excavation distances, excavation qeometries, number of foundation pits and construction procedure on the deformation of adjacent subway elevated structure is studied. The results show that, when the horizontal distance between foundation pit and structure is less than 2H (H represents the depth of the foundation pit), the lateral deformation of the structure is larger than that of vertical. The horizontal displacement and settlement of elevated bridge pier reach the maximum when horizontal distance is 1H. Besides, the additional deformation of subway viaduct piers increases rapidly with width of foundation pit. It decreases significantly when the width of foundation pit is larger than 8H. The depth of excavation of the foundation pit has the greatest influence on viaduct pier within 4H range of the central line of the foundation pit, especially when the excavation depth is more than 10 m. It is found that the structural deformation caused by multiple foundation pit construction shows obvious nonlinear superposition effect, while the construction procedure of multiple foundation pit has a slight influence on the total deformation of the structure.