The hydromechanical interaction of porous media with pore and free fluid widely exists in geotechnical engineering. In some situations, the solid phase would exhibit large deformation, and the boundaries between the solid and fluid phases might change substantially, making it challenging for computational simulation. A framework coupling the material point method (MPM) with the characteristic-based finite element method (CBFEM) was proposed for simulating the behavior of porous media and fluid systems with large deformation. It employs the MPM to discretize the solid domain and solve corresponding momentum equations in the Lagrangian framework in favor of its advantage for large deformation simulation, and the CBFEM to discretize the fluid domain and solve the Navier-Stokes and free-surface equations of the fluid phase in the Eulerian framework in favor of its maturity and high efficiency. The fractional-step approach was adopted to solve velocity and pressure separately in a time step to make the MPM-CBFEM coupling more flexible. In addition, an implicit drag-force term was proposed to grow the time step in undrained conditions. A series of quasi-static and transient problems were simulated to show the performance and prospects of the proposed framework for the large deformation of the porous media and fluid systems.