With the development and utilization of underground space resources, more and more deep foundation pits present the characteristics of deep excavation, large scale, irregular shape, etc., and their supporting structure design is complicated and construction is difficult, with obvious spatial effects. This paper takes a pit project of Nanjing subway as an example to analyze the impact of pit construction on neighboring bridges. The site is located in the lower reaches of the Yangtze River diffuse phase binary structure stratigraphy distribution section, the upper soft soil layer thickness is large, the lower pressurized aquifer water table is high, rich in water, geological conditions are very complex, the pit is a typical deep and large heterogeneous pit, away from the hyperbolic arch approach bridge is only 7.2 m, due to the bridge has been subjected to other underground engineering construction produced by a large deformation, the deformation that can be withstood is close to the critical value, so the subsequent project on the neighboring bridge. For this reason, the station pit support structure design based on the actual function of the underground space by setting partition wall partition excavation and MJS ultra-deep method wall comprehensive deformation control program. In this paper, by taking finite element numerical simulation to carry out the deformation prediction analysis of enclosure structure and bridge pile foundation caused by pit excavation in complex environment, the calculation results show that this deep, narrow and long shaped pit excavation has significant effect on settlement deformation of neighboring bridges, and the deformation control through the setup of partition wall subdividing excavation and MJS method wall can control the spatial effect of the pit and reduce the "long side effect", " heteromorphic effect" and other effects on the bridge settlement deformation. The feasibility of this comprehensive deformation control program is verified through the actual monitoring results of the on-site foundation pit excavation process. The research results are of good reference significance for the support and construction design of deep, narrow and long shaped foundation pits under similar complex geological conditions.