Abstract: The control of deformation in deep foundation pit retaining structures is crucial for construction safety. To investigate the deformation patterns of retaining structures in deep foundation pits constructed using the cover-excavation reverse construction method and to predict subsequent construction deformations, a study was conducted based on the Zhongyi Road subway station project in Wuhan. Focusing on five key construction stages—roof slab construction (Stage 1), road surface restoration (Stage 2), negative first floor construction (Stage 3), negative second floor construction (Stage 4), and base slab construction (Stage 5)—a three-dimensional finite element model of the station's deep foundation pit was established using ABAQUS software and validated against field monitoring data. Subsequently, the deformation patterns of the retaining structures in the cover-excavation reverse construction deep foundation pit were analyzed, and the deformations under subsequent construction stages were predicted. The results indicate that for construction stage 1, the absolute errors between the numerical simulations and the measured results are all within 1 mm, and the relative errors are within 15%. Furthermore, the trends of the simulation and measured data are consistent and exhibit good agreement, verifying the high computational accuracy of the established finite element model. This model can therefore be used to predict the deformation of deep foundation pit retaining structures in subsequent construction stages and to analyze the deformation characteristics of the retaining structures at different construction phases. For subsequent construction stages 2 to 5, the maximum horizontal displacements at monitoring points CX35 and CX51 range from 10.38 mm to 20.68 mm and 11.76 mm to 20.58 mm, respectively, both remaining below the warning threshold of 30 mm, indicating a safe and controllable condition. The established finite element model can be effectively applied to predict the deformation of deep foundation pit retaining structures in subsequent construction stages, and the findings of this study can serve as a reference for the analysis and prediction of retaining structure deformation in similar engineering projects.