Stone columns are being increasingly used as a cost-effective and environmentally friendly method for reinforcing soft soils of rail track embankments. Deformation behavior of stone columns reinforced soft clay has been the subject of an extensive number of experimental and modelling studies during last decades. A continuum-based numerical method provides valuable insights into the settlement, lateral deformation, stress and strain-rate dependent behavior of stone column at macroscopic scale. However, due to the discrete nature of stone columns, which are comprised of granular aggregates, they cannot be properly modelled by the continuum methods. This paper presents a novel coupling model of discrete element method (DEM) and finite difference method (FDM) to investigate the load-deformation behavior of stone columns considering micromechanical analysis. In the coupled discrete-continuum model, the soft soil domain under track embankment is modelled by the continuum method using FLAC and stone column is modelled by the discrete element method using PFC2D. A force-displacement transmission mechanism is introduced to achieve the interaction of both domains in which the DEM transfers forces and moment to the FDM and then the FDM updates displacements back to the DEM. The predicted load-deformation results are in good agreement with the data measured experimentally; indicating that the proposed coupling discrete-continuum model could capture the deformation behavior of stone column reinforced soft soils.