Stone columns are being increasingly used as a cost-effective and environmentally friendly method for improvement of weak soils. Deformation behavior of stone columns reinforced soft clay has been the subject of an extensive number of experimental and modelling studies during last decades. Continuum-based numerical models provide valuable insights into the settlement, lateral deformation, stress and strain-rate dependent behavior of stone column at macroscopic scale. However, owing to the discrete nature of stone columns, which are comprised of granular material, cannot be properly modelled by the continuum methods. This paper presents a coupled micro-macro method for numerically simulating a single stone column stabilized soft soils. A novel coupling model of discrete element method (DEM) and finite difference method (FDM) was introduced to investigate the load-deformation behavior of stone columns considering micromechanical analysis. In the coupled discrete-continuum model, the soft soil domain was modelled by the continuum method using FLAC and stone column was modelled by the discrete element method using PFC2D. A force-displacement transmission mechanism was 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 were 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.