Based on an ultra-deep circular shaft project in Shanghai, the field data of soil heave at the bottom of the pit during the construction were collected, and the vertical distribution pattern, evolution law and main influencing factors of soil heave at the bottom of the pit were summarized. An axisymmetric numerical model was then built and verified to investigate the effect of the excavation-induced unloading, dewatering, diaphragm wall and soil mechanical properties on the soil heave, then the mechanism of soil heave was revealed. Soil heave was the combined result of the soil mechanical response under the excavation-induced unloading, dewatering, and diaphragm wall restraint, in which the excavation-induced unloading and the deflection of the diaphragm wall caused the soil heave, and the dewatering and the negative frictional resistance inhibited the soil heave. Excavation-induced unloading had a prominent influence on the depth, and the unloading rebound mechanism dominated the soil heave within that depth, while the shear deformation controlled the soil heave beyond that depth range. Soil rheology and dissipation of negative pore water pressure jointly led to the time dependence of soil heave. The soil heave at the pit bottom of small-diameter ultra-deep shafts in soft soil areas decreased approximately linearly along the depth, and its maximum value was located at the center of the excavation face. The soil heave first increased slowly and then increased near linearly and rapidly with the increase of excavation depth. However, the soil heave tended to increase slowly with time in the non-excavation stage.