The land subsidence characteristics in Shanghai were constantly developing with the change of groundwater level in the process of urban development, and had different effects on the deformation of metro tunnels buried in deep soft soil layers. In this study, the long time series field monitoring data obtained by levelling and stratification extensometer methods was analyzed, and the coupling deformation mechanism of geological stratification and metro tunnel in deep quaternary coastal areas for different periods and scenarios was revealed. The results showed that with the rapid rise of the groundwater level in Shanghai since 2005, the deep sedimentary strata gradually rebound, resulting in the universal rebound of underground metro tunnel. The deformation trends of soil layers and metro tunnel structure were inconsistent with the regional land subsidence due to different control factors. For metro lines built in different periods, the tunnel displacement was basically controlled by the deformation of sedimentary strata below the tunnel structure. The coupling deformation of geological stratification and metro tunnel structure in the deep Quaternary sedimentary area can be described in three conceptual calculation models: inverse settlement model, extrusion model and counteract model. The hysteresis effects when the increase of water volume transformed to the rise of groundwater level and the soil layer deformation driven by rising water level were discussed.