This paper takes "nanjing typical section subway project" as the research object and uses FEFLOW numerical simulation software to establish unsteady flow numerical model. The magnitude of excavation inflow of subway is forecasted, and the dynamic changes of regional groundwater flow field after construction period, operation period and service expiration are studied and analyzes the influence of subway construction on the flow field of xianhemen water source and the possible environmental hydrogeological problems. The results show that the underground water level of the tunnel in the construction site and the tunnel in the section decreases greatly due to the water gushing and the need to drain the precipitation caused by the subway excavation, and the underground water flow field gradually returns to the initial state after the operation period and service expiration. The longwangshan section is the main section where the subway project has a great impact on xianhemen water source, while the other sections have a slight impact on the water source. However, the limestone in the research area from huashu station to longwang mountain area is buried shallow and karst is developed strongly. Therefore, subway engineering may lead to changes in runoff conditions in local areas and induce karst ground collapse disaster.