Large deformation in soils and frictional soil-structure contact are important geotechnical processes that should be considered when designing protective structures to cushion the impact of mass flows. In this paper, a numerical model combining the material point method and finite element method (MPM-FEM) is developed to simulate three-dimensional soil-structure interactions. In this model, soil with large deformation is discretized by using the MPM, while structures with small deformation are discretized by using the FEM. A hybrid contact method combining the advantages of point-point and point-segment contacts is used to model frictional soil-structure contact. In addition, to estimate energy dissipation properly, the Drucker-Prager model with the MiDi rheological relation is adopted as the constitutive model to characterize the dynamic characteristics of soil. The MPM-FEM is first validated for several geotechnical cases, including deformation of a flexible retaining wall and granular collapse, and achieves good agreement with an error smaller than 5.82%. Then, two numerical cases, i.e. impact of granular flow on a rigid structure and design of deformable structures, are studied by using the present model. It is demonstrated that the MPM-FEM model has potential applications in geotechnical engineering, especially when modelling the interaction between soil with large deformation and structures.