Excavation in foundation pits can result in serious issues for nearby tunnel structures like deformation, differential settlement, and seepage damage, which profoundly impact project timelines and potentially endanger life and property safety. Therefore, it is imperative to investigate these impacts before and after construction and to facilitate timely adjustments of construction measures and reinforcement where possible. In this study, a foundation pit construction project near a rail transit line is employed as a case to comprehensive study the impact of on-site deep foundation pit excavation on adjacent rail transit structures by numerical simulation. A three-dimensional finite-element model of the foundation pit based on site geological characteristics and construction procedures is established to study the excavation and maintenance processes. Through analysis of key parameters including soil deformation, displacement, shear force, and bending moment of the tunnel structures, the designed protective structure is found to have effectively mitigated soil deformation, ensuring the stability of the foundation pit. As excavation progresses, lateral soil deformation and vertical uplift gradually increase but remain within specified control values. During various excavation stages, the maximum displacement of the tunnel structure gradually increases, with the increase rates of maximum settlement being 29.09%, 20.51%, and 6.45%, respectively. This indicates a gradual enhancement of the stability of the tunnel structure. Additionally, excavation of the foundation pit has a significant impact on the bending moment distribution of the tunnel structure but does not affect the axial force and shear force of the tunnel structure. The findings of this study offer crucial scientific insights for evaluating the safety and stability of construction near tunnel structures.