Shanghai soft clay is a typical marine clay with specific structural characteristics. The tunnel and overlying soft clay may undergo repeated surface surcharge loading, such as the temporary soil stacking. Assessing the extent of structured soft clay deformation and tunnel displacement caused by repeated surface surcharge loading is of great significance for evaluating of the safety of ground structures and underground tunnels. In this study, the effects of repeated surface surcharge loading on the soil and tunnel displacement were numerically investigated. The finite element code DBLEAVES with an elasto-plastic constitutive model (Shanghai model) that describes the mechanical properties and structural characteristics of natural clay was used to simulate the soil response. The parameters of the constitutive model were obtained through geotechnical testing. The effects of the soil structural characteristics, seepage conditions, and loading conditions on the soil response and tunnel displacement were analyzed. The numerical results show that the maximum excess pore pressure of clay decreased as the number of loading cycles increased. The effects of the structural characteristics cause greater displacement, whereas the effects of the degradation parameters of the structure are more significant than the initial degree of the structure. The differences in the vertical displacement of the tunnel and overlying soils owing to the structural characteristics become apparent with an increase in surface surcharge loading. However, the effects of structural characteristics become less significant as the depth increases. The seepage conditions and loading method primarily affect the build-up of excess pore pressure and the development of effective stress paths. For soils inside the surcharge area, a flexible surcharge produces a greater vertical displacement than a rigid surcharge. As the burial depth increased, the effects of the seepage conditions and loading method showed a declining tendency.