In areas with soft soil, inrushing may occur during the construction of deep shaft structures under high water pressures, causing destructive accidents. Most studies on inrushing have used the finite element method. However, it is difficult to achieve a large deformation simulation because of mesh limitations. The material point method is not constrained by the mesh, and the material properties and motion information of the material are stored at the material points. Therefore, it can be used to effectively simulate large soil deformations. In this study, a numerical model for a deep shaft structure in Shanghai was formulated using the material point method to simulate the evolution of inrushing failure. The likelihood of inrushing damage at different excavation depths was analyzed. Soil heave at the bottom of the pit in the absence of inrushing was examined. The structural and environmental factors affecting the inrushing process are discussed. Strategies have been proposed from different perspectives, such as structure, environment, and construction methods, to reduce the damage caused by inrushing, thereby providing a reference for the safer construction of deep shaft structures.