This article combines numerical simulation and field monitoring methods to study the stability of the overlying Liuyang River embankment in the tunnel crossing between Huaqiao Station and Rice Museum Station of Changsha Metro’s Line 6. Using AutoCAD, 3Dmine, and COMSOL Multiphysics, a calculation model of the entire subway tunnel section crossing the flood control embankment under the coupling of fluids and solids was established. The process of tunnel-crossing the embankment and the variation in spatial displacement and plastic strain in different geological layers were analyzed from the perspective of time evolution and spatial distribution. The research results show that during the process of crossing the embankment, the deformation of the east bank is greater than that of the west bank, and crossing the west bank is the relatively riskier stage of the entire project. Moreover, during the process of crossing the embankment, the overlying soil layer will produce a plastic strain zone, and only a small amount of plastic strain is generated in the surrounding sandstone layer of the tunnel walls. In terms of the magnitude of plastic strain, the plastic strain area produced by the leading tunnel’s surrounding rocks is larger than that of the following tunnel. As the excavation progresses, a funnel-shaped settlement displacement gradually forms during the passage of the leading tunnel, and this settlement funnel gradually expands during the passage of the following tunnel, with the maximum settlement point transitioning from directly above the leading tunnel to the middle position between the two tunnels. Using the jitter filter algorithm and the adjacent average method to process the field monitoring data, the results show that the monitored deformation results well match the simulated settlement results.