Abstract: A rigid-flexible composite diaphragm wall system has been newly implemented in an ultra-deep excavation within the Yangtze River floodplain. In this system, the upper rigid diaphragm wall primarily controls lateral deformation, while the lower flexible section enhances seepage resistance by lengthening the groundwater bypass path, offering a cost-effective design strategy. This paper presents the engineering application of this system in a super-deep, large-scale excavation for a Nanjing metro station. Numerical analyses using PLAXIS 3D are conducted to investigate the support mechanism and optimize design parameters. Results indicate that, for a 70 m deep diaphragm wall, structural contribution below approximately 45 m is limited, allowing the use of lean concrete in the lower portion. The short-side diaphragm wall can safely extend to twice the excavation depth. For irregular wall geometries, the upper rigid section governs deformation control, whereas irregular long walls require increased rigid-section depth to satisfy safety criteria. Based on these findings, selected rigid walls were redesigned as rigid-flexible composite walls, achieving both deformation and seepage control while significantly reducing construction costs. The study provides valuable reference for similar ultra-deep excavation projects.